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At least 163 records · Page 9Linked to original sources

PubMed2005

VIS-O-BAC: exploratory visualization of functional genome studies from bacteria.

UNLABELLED: The visualization-aided exploration of complex datasets will allow the research community to formulate novel functional hypotheses leading to a better understanding of biological processes at all levels. Therefore, we have developed a web resource termed VIS-O-BAC designed for the functional investigation of expression data for model systems, such as bacterial pathogens based on a graphical display. Genome-scale datasets derived from typical 'omic' approaches can directly be explored with respect to three biologically relevant aspects, the genome structure (operon organization), the organization of genes in pathways (KEGG) and the gene function with Gene Ontology (GO) terms. The integrated viewers can be used in parallel and combine expression data and functional annotations from different external data repositories. The graphical visualizations evidently accelerate both the validation of regulatory information and the detection of affected biological processes. AVAILABILITY: http://leger2.gbf.de/cgi-bin/vis-o-bac.pl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Chromosome Mapping↗

PubMed1999

Applying the desiderata for controlled medical vocabularies to drug information databases.

Medication history has always been an integral part of the patient's medical record. With the advent of the computerized medical record and the longitudinal clinical data repository, having the medication history has enabled the development of clinical decision support system that alerts for drug to drug interactions and drug allergies. Furthermore, medication data is increasingly being analyzed from a utilization and clinical outcomes standpoint. For these activities to occur, a controlled pharmacy vocabulary akin to a controlled medical vocabulary is essential. Drug information databases are well-established sources of information for pharmacy-related data and products. However, do they measure up as a controlled vocabulary? Recent experience reviewing drug information databases and integrating pharmacy-related information into a data dictionary in real-time clinical use at multiple health care institutions have revealed several challenges and issues. These are discussed according to Cimino's desiderata for controlled medical vocabularies.

Databases, Factual↗

PubMed2005

Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004.

The increasing volume of proteomics data currently being generated by increasingly high-throughput methodologies has led to an increasing need for methods by which such data can be accurately described, stored and exchanged between experimental researchers and data repositories. Work by the Proteomics Standards Initiative of the Human Proteome Organisation has laid the foundation for the development of standards by which experimental design can be described and data exchange facilitated. The progress of these efforts, and the direct benefits already accruing from them, were described at a plenary session of the 3(rd) Annual HUPO congress. Parallel sessions allowed the three work groups to present their progress to interested parties and to collect feedback from groups already implementing the available formats.

China↗

PubMed2000

The phytophthora genome initiative database: informatics and analysis for distributed pathogenomic research.

The Phytophthora Genome Initiative (PGI) is a distributed collaboration to study the genome and evolution of a particularly destructive group of plant pathogenic oomycete, with the goal of understanding the mechanisms of infection and resistance. NCGR provides informatics support for the collaboration as well as a centralized data repository. In the pilot phase of the project, several investigators prepared Phytophthora infestans and Phytophthora sojae EST and Phytophthora sojae BAC libraries and sent them to another laboratory for sequencing. Data from sequencing reactions were transferred to NCGR for analysis and curation. An analysis pipeline transforms raw data by performing simple analyses (i.e., vector removal and similarity searching) that are stored and can be retrieved by investigators using a web browser. Here we describe the database and access tools, provide an overview of the data therein and outline future plans. This resource has provided a unique opportunity for the distributed, collaborative study of a genus from which relatively little sequence data are available. Results may lead to insight into how better to control these pathogens. The homepage of PGI can be accessed at http:www.ncgr.org/pgi, with database access through the database access hyperlink.

Databases, Factual↗

PubMed2000

Clinical trials in developing countries: Discussions at the '9th International Symposium on Long Term Clinical Trials', London, UK, 19-20 June 2000.

This symposium provided a useful forum for the discussion of issues relating to the design and conduct of clinical trials. There is a need for greater awareness of the complexity of modern day trials, in which a host of statistical, logistical, regulatory and ethical issues are involved. Issues discussed ranged from the effect of sample size on the outcome, and subgroup analysis, to defining and maintaining discrete endpoints. Some useful debate centred on the use of meta-analysis and the current limitations of combining information from different data sets. This brought up the subjects of trial registries and raw data repositories for all clinical trials. Progress and relevance of the Cochrane collaboration were reviewed. The economics of clinical trials was another important topic. Regulatory issues such as the role of data and safety monitoring boards (DSMB) and the guidelines in place for effective data monitoring and progress analysis were discussed. Representatives of government organisations and industry gave both European and American perspectives. This report however focuses specifically on the section devoted to the subject of clinical trials in developing countries.

Journal Article↗

PubMed1995

The PLDD registry.

The rapid acceptance of minimally invasive surgery in the United States has largely occurred without statistical proof of its superiority over traditional methods. All players in the healthcare field now see the need for valid outcome studies supporting the efficacy of new treatment techniques. Percutaneous laser disc decompression (PLDD) will gain wide acceptance only if it is statistically shown to be a safe and effective alternative treatment of a lumbar disc herniation. To that end, a central PLDD registry has been developed and implemented into clinical practice at several centers. This article reviews healthcare trends that motivated the creation of this data repository and discusses the history of its development. The currently used PLDD evaluation form is outlined and its utility is discussed. Most importantly, preliminary PLDD results and complications based on the data received are presented and analyzed.

Diskectomy, Percutaneous↗

PubMedDate not supplied

Factors affecting adolescent reproductive health in Manitoba.

OBJECTIVES: To report teen pregnancy and sexually transmitted infections (STI) rates among Manitoba adolescents, and associated factors including rates of sexual intercourse and contraceptive use. METHODS: Teen pregnancy rates in females aged 15 to 19 for the fiscal years 1994/95 through 1998/99 were derived from the Population Health Research Data Repository and reported by geographical areas and income quintiles. Premature mortality rate (PMR) and the Socioeconomic Factor Index (SEFI) measured the overall health and socioeconomic well-being of regional populations. Data on sexual activity and contraceptive use were derived from the 1996 National Population Health Survey for males and females ages 15 through 19 years. RESULTS: The teen pregnancy rate for Manitoba was 63.2/1000, varying by geography and inversely correlated with income, PMR, and SEFI. 39% (95% CI 33-45) of teens reported sexual intercourse, with higher rates in urban areas (46%, 95 % CI 35-57) and the North (48%, 95% CI 36-60) compared to South Rural (30%, 95% CI 25-34), and in low-income families (68%, 95% CI 53-83) compared with middle/high (33%, 95% CI 26-40). For sexually active females, 42% (95% CI 28-57) used the birth control pill, with higher rates in low-income families (70%, 95% CI 50-90) compared to middle/high income (31%, 95% CI 14-48). Condom use (at last sexual intercourse) was reported by 82% (95% CI 72-92) of adolescents, with trends (though not statistically significant) to lower use in low-income families and the North. CONCLUSION: Reliance on the pill for contraception, combined with low rates of condom use, are public health concerns for adolescents where STI and unintended pregnancy rates are high.

Adolescent↗

PubMed2004

Advances in the development of common interchange standards for proteomic data.

The generation of proteomics data is increasingly high-throughput and high volume. Both experimental design and the technologies used to produce and subsequently analyze the data are becoming ever more complex. An increasing need for methods by which such data can be accurately described, stored and exchanged between experimenters and data repositories has been recognised. Work by the Proteomics Standards Initiative of the Human Proteome Organisation has laid the foundation for the development of standards by which experimental design can be described and data exchange facilitated. At a recent workshop in Nice, participants gathered to review the progress made to date and assist in pushing the process still further forward.

Humans↗

PubMed2004

Current status of proteomic standards development.

The generation of proteomic data is becoming ever more high throughput. Both the technologies and experimental designs used to generate and analyze data are becoming increasingly complex. The need for methods by which such data can be accurately described, stored and exchanged between experimenters and data repositories has been recognized. Work by the Proteome Standards Initiative of the Human Proteome Organization has laid the foundation for the development of standards by which experimental design can be described and data exchange facilitated. The Minimum Information About a Proteomic Experiment data model describes both the scope and purpose of a proteomics experiment and encompasses the development of more specific interchange formats such as the mzData model of mass spectrometry. The eXtensible Mark-up Language-MI data interchange format, which allows exchange of molecular interaction data, has already been published and major databases within this field are supplying data downloads in this format.

Databases, Protein↗

PubMed2003

WormBase: a cross-species database for comparative genomics.

WormBase (http://www.wormbase.org/) is a web-accessible central data repository for information about Caenorhabditis elegans and related nematodes. The past two years have seen a significant expansion in the biological scope of WormBase, including the integration of large-scale, genome-wide data sets, the inclusion of genome sequence and gene predictions from related species and active literature curation. This expansion of data has also driven the development and refinement of user interfaces and operability, including a new Genome Browser, new searches and facilities for data access and the inclusion of extensive documentation. These advances have expanded WormBase beyond the obvious target audience of C. elegans researchers, to include researchers wishing to explore problems in functional and comparative genomics within the context of a powerful genetic system.

Animals↗

PubMed2005

Evaluation of the association between the EQ-5D (health-related utility) and body mass index (obesity) in hospital-treated people with Type 1 diabetes, Type 2 diabetes and with no diagnosed diabetes.

AIMS: The purpose of this study was to characterize the impact of body mass index (BMI) on health-related utility for patients with Type 1 and Type 2 diabetes and those without diabetes. METHODS: The study was conducted in Cardiff and the Vale of Glamorgan, Wales, UK. Health-related utility was measured using the EQ-5D(index). Patients from the Health Outcomes Data Repository (HODaR) were surveyed by postal questionnaire either 6 weeks post discharge for in-patients or at out-patient clinics between January 2002 and July 2003. BMI was calculated from self-reported data within the survey. Patients with diabetes were identified by a previous history of an in-patient admission with diabetes or as an out-patient with diabetes recorded as a coexisting diagnosis. RESULTS: Questionnaires were returned from 27 924 patients of whom 2575 had diabetes. Increasing BMI was found to reduce utility in all three groups. BMI was significantly greater for those with Type 2 diabetes compared with those with Type 1, and those without diabetes (P < 0.001). Multiple regression analysis demonstrated that both BMI and diabetes status had a significant effect on utility. However, the rate of change of utility attributable to BMI was not found to be significantly different between the various groups. CONCLUSIONS: Obesity negatively impacts upon health-related utility and thus quality of life for all patient groups. There was no significant difference in the effect of obesity on utility between those with and without diabetes.

Adolescent↗

PubMed2002

Cancer biomarkers: easier said than done.

BACKGROUND: Biological and technical advances have led to greatly increased research and development of cancer biomarkers. This overview lists some of the challenges and barriers to developing novel effective cancer biomarkers and enablers to facilitate cancer biomarker development. METHODS: Current scientific literature regarding development of biomarkers for cancer and other diseases was reviewed. RESULTS: Challenges to developing cancer biomarkers include better understanding of biological heterogeneity, including host/tumor heterogeneity; analytical factors, such as interferences and analytical sensitivity; clinical pathologic factors, such as current histopathologic standards; and health service and market factors. More standardized biomarker definitions, standardization of cancer biology terminology, and high-quality reference materials (specimen and clinical data repositories) were identified as factors required to support advances in cancer biomarkers. CONCLUSIONS: With the above enablers, novel cancer biomarkers may be useful, both for assessing early and established neoplasia more precisely and for contributing data toward development of novel practical concepts regarding cancer biology.

Biomarkers, Tumor↗

PubMed1996

A decision-supported outpatient practice system.

We describe a Decision-supported Outpatient Practice (DOP) system developed and now in use at the Columbia-Presbyterian Medical Center. DOP is an automated ambulatory medical record system that integrates in-patient and ambulatory care data, and incorporates active and passive decision support mechanisms with a view towards improving the quality of primary care. Active decision support occurs in the form of event-driven reminders created within a remote clinical information system with its central data repository and decision support system (DSS). Novel features of DOP include patient specific health maintenance task lists calculated by the remote DSS. uses of a semantically structured controlled medical vocabulary to support clinical results review and provider data entry, and exploitation of an underlying ambulatory data model that provides for an explicit record of evolution of insight regarding patient management. Benefits, challenges, and plans are discussed.

Ambulatory Care Facilities↗

PubMedDate not supplied

Update on patient privacy legislation.

The administrative simplification provisions of HIPAA will establish the first national standards for the electronic transmission of health care transactions with which all federal programs (DOD, Medicare, and Medicaid) and all private health plans must comply. Individuals and organizations should prepare themselves, their systems, and their processes to meet these new administrative and financial data standards and requirements. The benefits of standardized electronic transactions on achieving a single paper-free claims submission to be used by all providers and payers is of obvious benefit. Not so obvious are consequences associated with limiting the access and use of existing data repositories on a variety of clinical, administrative, and research functions. It is critically important in this age of increased accountability for fiscal restraint and improving the outcomes of entire patient populations that clinicians, managers, organizations, and researchers to use data for a variety of clinical, quality improvement/evaluation, and research purposes. Administrative simplification and protecting individual privacy should not be achieved by overly bureaucratic and restrictive responses that impede epidemiologic and health services research, quality improvement activities, and optimization strategies for improving the health of populations. While the health system understands the need for some increased regulation to ensure the privacy of individual patient privacy in the "wired" world solutions must be found and overly restrictive consequences associated with prohibiting access to data must be resolved. More than ever, the entire system requires data to inform every level and type of decision made. Legislation and bureaucratic processes that do not understand and support responsible data-driven decision-making will serve to roll-back, not advance health system improvement. As we prepare ourselves for HIPAA compliance and the expectations of the benefits it will achieve, we must wait to see what impact it will have on clinical, administrative, and research functions concerned with improvement.

Computer Security↗

PubMed1999

The Regenstrief Medical Record System: a quarter century experience.

Entrusted with the records for more than 1.5 million patients, the Regenstrief Medical Record System (RMRS) has evolved into a fast and comprehensive data repository used extensively at three hospitals on the Indiana University Medical Center campus and more than 30 Indianapolis clinics. The RMRS routinely captures laboratory results, narrative reports, orders, medications, radiology reports, registration information, nursing assessments, vital signs, EKGs and other clinical data. In this paper, we describe the RMRS data model, file structures and architecture, as well as recent necessary changes to these as we coordinate a collaborative effort among all major Indianapolis hospital systems, improving patient care by capturing city-wide laboratory and encounter data. We believe that our success represents persistent efforts to build interfaces directly to multiple independent instruments and other data collection systems, using medical standards such as HL7, LOINC, and DICOM. Inpatient and outpatient order entry systems, instruments for visit notes and on-line questionnaires that replace hardcopy forms, and intelligent use of coded data entry supplement the RMRS. Physicians happily enter orders, problems, allergies, visit notes, and discharge summaries into our locally developed Gopher order entry system, as we provide them with convenient output forms, choice lists, defaults, templates, reminders, drug interaction information, charge information, and on-line articles and textbooks. To prepare for the future, we have begun wrapping our system in Web browser technology, testing voice dictation and understanding, and employing wireless technology.

Computer Terminals↗

PubMedDate not supplied

Data mining as a tool for research and knowledge development in nursing.

The ability to collect and store data has grown at a dramatic rate in all disciplines over the past two decades. Healthcare has been no exception. The shift toward evidence-based practice and outcomes research presents significant opportunities and challenges to extract meaningful information from massive amounts of clinical data to transform it into the best available knowledge to guide nursing practice. Data mining, a step in the process of Knowledge Discovery in Databases, is a method of unearthing information from large data sets. Built upon statistical analysis, artificial intelligence, and machine learning technologies, data mining can analyze massive amounts of data and provide useful and interesting information about patterns and relationships that exist within the data that might otherwise be missed. As domain experts, nurse researchers are in ideal positions to use this proven technology to transform the information that is available in existing data repositories into useful and understandable knowledge to guide nursing practice and for active interdisciplinary collaboration and research.

Algorithms↗

PubMed2006

An XML-based system for synthesis of data from disparate databases.

Diverse data sets have become key building blocks of translational biomedical research. Data types captured and referenced by sophisticated research studies include high throughput genomic and proteomic data, laboratory data, data from imagery, and outcome data. In this paper, the authors present the application of an XML-based data management system to support integration of data from disparate data sources and large data sets. This system facilitates management of XML schemas and on-demand creation and management of XML databases that conform to these schemas. They illustrate the use of this system in an application for genotype-phenotype correlation analyses. This application implements a method of phenotype-genotype correlation based on phylogenetic optimization of large data sets of mouse SNPs and phenotypic data. The application workflow requires the management and integration of genomic information and phenotypic data from external data repositories and from the results of phenotype-genotype correlation analyses. Our implementation supports the process of carrying out a complex workflow that includes large-scale phylogenetic tree optimizations and application of Maddison's concentrated changes test to large phylogenetic tree data sets. The data management system also allows collaborators to share data in a uniform way and supports complex queries that target data sets.

Animals↗

PubMed1996

Analysis of the recurrence patterns for nonsyndromic cleft lip with or without cleft palate in the families of 3,073 Danish probands.

The identification of several putative susceptibility loci for nonsyndromic cleft lip with or without cleft palate (CL +/- P) has sparked a renewed interest in the genetics of this condition. However, prior to undertaking linkage studies for complex traits such as CL +/- P it is desirable to have some understanding of the number and nature of the loci involved in disease susceptibility. The ability to obtain valid estimates of these parameters is contingent on the availability of family data which are unbiased by factors that distort the true familial recurrence pattern. In an effort to obtain such data, 2 centralized data repositories (the Danish Central Person Registry and the Danish Facial Cleft Database), were linked and used to estimate the risks to first, second, and third-degree relatives of 3,073 CL +/- P probands born in Denmark from 1952 to 1987. Analyses of these data excluded single locus and additive multilocus inheritance of CL +/- P, and provided evidence that CL +/- P is most likely determined by the effects of multiple interacting loci. Under a multiplicative model, no single locus can account for more than a threefold increase in the risk to first-degree relatives of CL +/- P probands. These data provide further evidence that nonparametric linkage methods (ex. affected relative pair studies) are likely to represent a more realistic approach for identifying CL +/- P susceptibility loci, than are traditional pedigree-based methods. However, at least 100 and more realistically several hundred (300-500) affected sib pairs are likely to be required to detect linkage to CL +/- P susceptibility loci.

Cleft Lip↗