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At least 325 records · Page 18Linked to original sources

PubMed1978

Protocol for a computed tomography scanner performance repository.

An argument is presented for organization of a Computed Tomography Scanner Performance Repository. Performance data on CT scanners would be distributed in statistical form to the radiological community. A Protocol is presented for the uniform collection of data. Results of exposure, resolution and visibility measurements made by the authors are presented for the EMI 5005/U, Pfizer 0200 FS and General Electric CT/T scanners.

Humans↗

PubMed1998

GDB: the Human Genome Database.

The Genome Database (GDB, http://www.gdb.org ) is a public repository of data on human genes, clones, STSs, polymorphisms and maps. GDB entries are highly cross-linked to each other, to literature citations and to entries in other databases, including the sequence databases, OMIM, and the Mouse Genome Database. Mapping data from large genome centers and smaller mapping efforts are added to GDB on an ongoing basis. The database can be searched by a variety of methods, ranging from keyword searches to complex queries. Major functionality extensions in the last year include the ongoing computation of integrated human genome maps, called Comprehensive Maps, and the use of those maps to support positional queries and graphic displays. The capabilities of the GDB map viewer (Mapview) have been extended to include map printing and the graphical display of ad hoc query results. The HUGO Nomenclature Committee continues to curate the proposed and official gene symbols and related data in collaboration with GDB. As genome research shifts its emphasis from mapping to sequencing and functional analysis, the scope of the GDB schema is being extended. We are in the process of adding representations of gene function and expression, and improving our representation of human polymorphism and mutation.

Animals↗

PubMed2003

ArrayExpress--a public repository for microarray gene expression data at the EBI.

ArrayExpress is a new public database of microarray gene expression data at the EBI, which is a generic gene expression database designed to hold data from all microarray platforms. ArrayExpress uses the annotation standard Minimum Information About a Microarray Experiment (MIAME) and the associated XML data exchange format Microarray Gene Expression Markup Language (MAGE-ML) and it is designed to store well annotated data in a structured way. The ArrayExpress infrastructure consists of the database itself, data submissions in MAGE-ML format or via an online submission tool MIAMExpress, online database query interface, and the Expression Profiler online analysis tool. ArrayExpress accepts three types of submission, arrays, experiments and protocols, each of these is assigned an accession number. Help on data submission and annotation is provided by the curation team. The database can be queried on parameters such as author, laboratory, organism, experiment or array types. With an increasing number of organisations adopting MAGE-ML standard, the volume of submissions to ArrayExpress is increasing rapidly. The database can be accessed at http://www.ebi.ac.uk/arrayexpress.

Animals↗

PubMed1999

Databases in MS research: pitfalls and promises.

A database is an organized repository of data. Prospective collection of patient information in a database ('databasing') has been attempted by a few consortia of MS investigators over the past 10 years. This approach promises to facilitate epidemiologic research in MS and investigation of the natural history of the disease and how it might be altered by long-term treatments such as interferon beta. Databasing has some advantages over clinical trials in assessing new therapies, primarily because the focus is on long-term effectiveness in an entire population rather than short-term statistical significance in a highly selected population. The limitations of databasing and strategies to overcome these limitations are addressed.

Clinical Trials as Topic↗

PubMed2002

Association of IL4R haplotypes with type 1 diabetes.

We have investigated, in 282 multiplex Caucasian families (the Human Biological Data Interchange Repository), the association of type 1 diabetes with polymorphisms in the IL4R gene. IL4R encodes a subunit of the interleukin-4 receptor, a molecule critical to T-helper cell development. By genotyping eight different IL4R single-nucleotide polymorphisms (SNPs) and identifying haplotypes (complex alleles) in the multiplex type 1 diabetic families who were stratified for HLA genotype, we have observed significant evidence of linkage and association of the IL4R gene to type 1 diabetes. In particular, we have identified a specific haplotype that appears to be protective and observed that this protective effect is strongest among individuals not carrying the HLA DR3/DR4 genotype (which confers the strongest genetic risk for type 1 diabetes). These findings suggest an important role for the IL4R gene in immune-related disease susceptibility and illustrate the value of using multi-SNP haplotype information in association studies.

Alleles↗

PubMed2004

Integration of Web-based and PC-based clinical research databases.

UNLABELLED: We have created a Web-based repository or data library of information about measurement instruments used in studies of multi-factorial geriatric health conditions (the Geriatrics Research Instrument Library - GRIL) based upon existing features of two separate clinical study data management systems. GRIL allows browsing, searching, and selecting measurement instruments based upon criteria such as keywords and areas of applicability. Measurement instruments selected can be printed and/or included in an automatically generated standalone microcomputer database application, which can be downloaded by investigators for use in data collection and data management. METHODS: Integration of database applications requires the creation of a common semantic model, and mapping from each system to this model. Various database schema conflicts at the table and attribute level must be identified and resolved prior to integration. Using a conflict taxonomy and a mapping schema facilitates this process. RESULTS: Critical conflicts at the table level that required resolution included name and relationship differences. CONCLUSIONS: A major benefit of integration efforts is the sharing of features and cross-fertilization of applications created for similar purposes in different operating environments. Integration of applications mandates some degree of metadata model unification.

Aged↗

PubMed1977

Current cooperative clinical trials in the non-Hodgkin's lymphomas.

Current cooperative group trails in non-Hodgkin's lymphoma have been analyzed for their overall methods and strategies. There has been more frequent application of staging procedures and individualization of protocols for favorable and unfavorable histologies according to the Rappaport classification. Early-stage protocols are evaluating the extent of radiotherapy and the need for chemotherapy as maintenance. In later stages the incorporation of new agents in induction regimens, use of cycle-active agents, development of non-cross-resistant combinations, and use of radiation in bulk disease are being examined. In childhood lymphoma, strategies using both leukemia- or lymphoma-type approaches are being tested. Cooperative group trials should also serve as an extensive repository of data on late effects of treatment and on alterations of the course of the disease for future analysis.

Adult↗

PubMedDate not supplied

Good Automated Laboratory Practices and other standards: validation of computer systems in the PC environment.

In summary, the validation of purchased software and add-on programs requires careful examination of the situation to determine the most effective and logical methods. A standard validation methodology that is used for larger systems would be difficult and possibly dangerous to employ for a PC system because of the significant differences between the environments. It should be noted, however, that there are almost daily changes in the computer software industry. A number of potential solutions have emerged over the past few years that can be applied to reduce the concerns caused by the apparently insufficient controls in the PC environment. For example, currently available technologies would permit multiple PC users to access a secure central application or repository of data and prevent them from making changes to a validated system or database. A properly designed system could enable these distributed users to use the data to perform their required functions, while maintaining a validated state.

Clinical Laboratory Information Systems↗

PubMed2004

Experimental Peptide Identification Repository (EPIR): an integrated peptide-centric platform for validation and mining of tandem mass spectrometry data.

LC MS/MS has become an established technology in proteomic studies, and with the maturation of the technology the bottleneck has shifted from data generation to data validation and mining. To address this bottleneck we developed Experimental Peptide Identification Repository (EPIR), which is an integrated software platform for storage, validation, and mining of LC MS/MS-derived peptide evidence. EPIR is a cumulative data repository where precursor ions are linked to peptide assignments and protein associations returned by a search engine (e.g. Mascot, Sequest, or PepSea). Any number of datasets can be parsed into EPIR and subsequently validated and mined using a set of software modules that overlay the database. These include a peptide validation module, a protein grouping module, a generic module for extracting quantitative data, a comparative module, and additional modules for extracting statistical information. In the present study, the utility of EPIR and associated software tools is demonstrated on LC MS/MS data derived from a set of model proteins and complex protein mixtures derived from MCF-7 breast cancer cells. Emphasis is placed on the key strengths of EPIR, including the ability to validate and mine multiple combined datasets, and presentation of protein-level evidence in concise, nonredundant protein groups that are based on shared peptide evidence.

Breast Neoplasms↗

PubMed2005

Towards data warehousing and mining of protein unfolding simulation data.

OBJECTIVES: The prediction of protein structure and the precise understanding of protein folding and unfolding processes remains one of the greatest challenges in structural biology and bioinformatics. Computer simulations based on molecular dynamics (MD) are at the forefront of the effort to gain a deeper understanding of these complex processes. Currently, these MD simulations are usually on the order of tens of nanoseconds, generate a large amount of conformational data and are computationally expensive. More and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. METHODS: To adequately organize, manage, and analyze the data generated by unfolding simulation studies, we designed a data warehouse system that is embedded in a grid environment to facilitate the seamless sharing of available computer resources and thus enable many groups to share complex molecular dynamics simulations on a more regular basis. RESULTS: To gain insight into the conformational fluctuations and stability of the monomeric forms of the amyloidogenic protein transthyretin (TTR), molecular dynamics unfolding simulations of the monomer of human TTR have been conducted. Trajectory data and meta-data of the wild-type (WT) protein and the highly amyloidogenic variant L55P-TTR represent the test case for the data warehouse. CONCLUSIONS: Web and grid services, especially pre-defined data mining services that can run on or 'near' the data repository of the data warehouse, are likely to play a pivotal role in the analysis of molecular dynamics unfolding data.

Computational Biology↗

PubMed2001

Mining association rules from clinical databases: an intelligent diagnostic process in healthcare.

Data mining is the process of discovering interesting knowledge, such as patterns, associations, changes, anomalies and significant structures, from large amounts of data stored in databases, data warehouses, or other information repositories. Mining Associations is one of the techniques involved in the process mentioned above and used in this paper. Association is the discovery of association relationships or correlations among a set of items. The algorithm that was implemented is a basic algorithm for mining association rules, known as a priori. In Healthcare, association rules are considered to be quite useful as they offer the possibility to conduct intelligent diagnosis and extract invaluable information and build important knowledge bases quickly and automatically. The problem of identifying new, unexpected and interesting patterns in medical databases in general, and diabetic data repositories in specific, is considered in this paper. We have applied the a priori algorithm to a database containing records of diabetic patients and attempted to extract association rules from the stored real parameters. The results indicate that the methodology followed may be of good value to the diagnostic procedure, especially when large data volumes are involved. The followed process and the implemented system offer an efficient and effective tool in the management of diabetes. Their clinical relevance and utility await the results of prospective clinical studies currently under investigation.

Algorithms↗

PubMed2006

Six methodological steps to build medical data warehouses for research.

PURPOSE: We propose a simple methodology for heterogeneous data collection and central repository-style database design in healthcare. Our method can be used with or without other software development frameworks, and we argue that its application can save a relevant amount of implementation effort. Also, we believe that the method can be used in other fields of research, especially those that have a strong interdisciplinary nature. BACKGROUND: The idea emerged during a healthcare research project, which consisted among others in grouping information from heterogeneous and distributed information sources. We developed this methodology by the lessons learned when we had to build a data repository, containing information about elderly patients flows in the UK's long-term care system (LTC). DESIGN: We explain thoroughly those aspects that influenced the methodology building. The methodology is defined by six steps, which can be aligned with various iterative development frameworks. We describe here the alignment of our methodology with the RUP (rational unified process) framework. The methodology emphasizes current trends, as early identification of critical requirements, data modelling, close and timely interaction with users and stakeholders, ontology building, quality management, and exception handling. RESULTS: Of a special interest is the ontological engineering aspect, which had the effects with the highest impact after the project. That is, it helped stakeholders to perform better collaborative negotiations that brought better solutions for the overall system investigated. An insight into the problems faced by others helps to lead the negotiators to win-win situations. We consider that this should be the social result of any project that collects data for better decision making that leads finally to enhanced global outcomes.

Computer Communication Networks↗

PubMed2004

Sequence-structure mapping errors in the PDB: OB-fold domains.

The Protein Data Bank (PDB) is the single most important repository of structural data for proteins and other biologically relevant molecules. Therefore, it is critically important to keep the PDB data, as much as possible, error-free. In this study, we have analyzed PDB crystal structures possessing oligonucleotide/oligosaccharide binding (OB)-fold, one of the highly populated folds, for the presence of sequence-structure mapping errors. Using energy-based structure quality assessment coupled with sequence analyses, we have found that there are at least five OB-structures in the PDB that have regions where sequences have been incorrectly mapped onto the structure. We have demonstrated that the combination of these computation techniques is effective not only in detecting sequence-structure mapping errors, but also in providing guidance to correct them. Namely, we have used results of computational analysis to direct a revision of X-ray data for one of the PDB entries containing a fairly inconspicuous sequence-structure mapping error. The revised structure has been deposited with the PDB. We suggest use of computational energy assessment and sequence analysis techniques to facilitate structure determination when homologs having known structure are available to use as a reference. Such computational analysis may be useful in either guiding the sequence-structure assignment process or verifying the sequence mapping within poorly defined regions.

Amino Acid Sequence↗

PubMed1991

Electronic data publishing and GenBank.

GenBank, the national repository for nucleotide sequence data, has implemented a new model of scientific data management, which we term electronic data publishing. In traditional publishing, both scientific conclusions and supporting data are communicated via the printed page, and in electronic journal publishing, both types of information are communicated via electronic media. In electronic data publishing, by contrast, conclusions are published in a journal while data are published via a network-accessible, electronic database.

Base Sequence↗

PubMed1998

Use of 3D QSAR methodology for data mining the National Cancer Institute Repository of Small Molecules: application to HIV-1 reverse transcriptase inhibition.

A three-dimensional (3D) stereoelectronic pharmacophore developed from a 3D quantitative structure-activity relationship (QSAR) investigation formed the basis of the development of a two-phase data-mining methodology to uncover novel leads to inhibit human immunodeficiency virus type 1 (HIV-1) reverse transcriptase at the nonnucleoside binding site. The database searching phase employed a field search for ligand requirements (such as log P, molecular volume) that were accessible from the database keys. Next, a 3D database search was performed that used an automated fitting procedure and the calculation of several binding parameters. These binding parameters were used to test the hits by a discriminant function that was previously trained to recognize active from inactive analogs. During the structural evaluation phase of the methodology, conformational properties and complementary receptor features of the hits were examined by 2D and 3D evaluations, which were followed by molecular modeling investigations. When this method was applied to a test database, an improvement from 6.4% to 100% active analogs was achieved.

Database Management Systems↗

PubMed1990

Managing clinical research data: software tools for hypothesis exploration.

Data representation, data file specification, and the communication of data between software systems are playing increasingly important roles in clinical data management. This paper describes the concept of a self-documenting file that contains annotations or comments that aid visual inspection of the data file. We describe access of data from annotated files and illustrate data analysis with a few examples derived from the UNIX operating environment. Use of annotated files provides the investigator with both a useful representation of the primary data and a repository of comments that describe some of the context surrounding data capture.

Data Interpretation, Statistical↗

PubMed2001

Integrated patient data for optimal patient management: the value of laboratory data in quality improvement.

Managed care organizations are shifting from traditional utilization management programs to focus on initiatives that improve the health of an insured population. This strategy requires sophisticated data integration to identify at-risk individuals and track outcomes. Laboratory data are becoming increasingly valuable tools for managed care organizations and healthcare providers. The HEDIS Effectiveness of Care measures have incorporated laboratory data into several key performance indicators. By building a comprehensive repository of laboratory data that includes both procedure codes and laboratory values, managed care organizations can realize substantial savings by avoiding the costly medical record reviews required when administrative data are incomplete. In addition to tracking clinical outcomes, laboratory data provide the ability to risk-stratify a population to target high-risk individuals for case management and disease management interventions. Healthcare organizations face several challenges in the integration of laboratory data into medical databases and practice management software. Confidentiality is a key consideration in view of recent healthcare regulations. Providers of laboratory services should work collaboratively with organizations setting standards for healthcare informatics to facilitate the pooling of data for quality improvement and outcomes research. Health Level Seven, Inc. (HL7), Logical Observation Identifier Names and Codes (LOINC), and Systematized Nomenclature of Medicine (SNOMED) will likely play a key role in this process.

Clinical Laboratory Techniques↗

PubMed2006

IntAct--open source resource for molecular interaction data.

IntAct is an open source database and software suite for modeling, storing and analyzing molecular interaction data. The data available in the database originates entirely from published literature and is manually annotated by expert biologists to a high level of detail, including experimental methods, conditions and interacting domains. The database features over 126,000 binary interactions extracted from over 2100 scientific publications and makes extensive use of controlled vocabularies. The web site provides tools allowing users to search, visualize and download data from the repository. IntAct supports and encourages local installations as well as direct data submission and curation collaborations. IntAct source code and data are freely available from http://www.ebi.ac.uk/intact.

DNA↗