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At least 343 records · Page 19Linked to original sources
PubMed2002

The EMBL Nucleotide Sequence Database.

The EMBL Nucleotide Sequence Database (aka EMBL-Bank; http://www.ebi.ac.uk/embl/) incorporates, organises and distributes nucleotide sequences from all available public sources. EMBL-Bank is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collaboration with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis. Major contributors to the EMBL database are individual scientists and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via FTP, email and World Wide Web interfaces. EBI's Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many other specialized databases. For sequence similarity searching, a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. All resources can be accessed via the EBI home page at http://www.ebi.ac.uk.

Animals↗
PubMed1986

BACOMP--database of bioactive compounds for structure-activity relationship.

BACOMP database is presented for structure-activity relationship (SAR) investigations; it was realized on a BK-1300 general purpose microcomputer using the MICRO-SETOR network database management system. Some general considerations of database design are given and the models and facilities for a development of a microcomputer-based SAR oriented database are described. The database contains the following information for the bioactive compounds: chemical structures, biological activities, trade names, reference numbers and information sources. For computer representation of chemical structures SAR oriented language is used. The database software includes: system software, data capture and data editing software, information retrieval and data processing applications. The software development is done in FORTRAN IV and MACRO assembly language. The programs are written in a completely interactive mode. The information retrieval software includes 12 functions giving an information for the database as a whole and for a single compound as well. The data processing software includes 8 functions for finding common structural fragments among compounds with similar biological activity and for estimating a structural similarity between different compounds. The functions are selected from corresponding screen MENUs. The function realization results are framed as appropriate screen formats and the receipt of hardcopies is available. The database can be used to develop predictive methods in respect of the investigated biological activity.

Drug Information Services↗
PubMed2004

Initial twelve months experience and analysis for 2001-2002 from the Australasian Society of Cardiac and Thoracic Surgeons--Victorian database project.

UNLABELLED: The Australasian Society of Cardiac and Thoracic Surgeons (ASCTS) have established a database for the collection and analysis of the results of cardiac surgery in Australia and New Zealand. Initially data has been collected only in Victoria public hospitals. This report covers the first 12 months of data collection from 1st August 2001 to 1st July 2002. BACKGROUND: Whilst cardiac surgical performance in Australia is considered to be of a high standard equivalent to other developed countries, there is currently no systematic approach to data collection in order to provide performance indicators and benchmarks. The development of an Australasian cardiac surgical database and performance indicators will enable benchmarking and comparison with international standards which should lead to performance improvements. METHODS: A database definition set and standardised data collection form was developed by the ASCTS for all participating cardiac surgery units in public hospitals in Victoria. Opt-off consent for subject inclusion in the database was approved by each participating institutional ethics review committee. An electronic database and reporting application was developed. Data included in this analysis is from the initial 12 months collection from all hospitals participating in the project from 1st August 2001 to 31st July 2002. RESULTS: Overall, there were 2982 procedures performed in this period of which 2969 had sufficient data to be included in this analysis (99.5%). The majority of procedures 2017 (68%) being undertaken were isolated coronary artery bypass surgery (CABG). The mean age of all subjects undergoing procedures was 65 years (range: 18-91 years) and 70% were male. 64% of all procedures were elective and 6.1% emergency or salvage. Median post-procedure length of hospital stay for all procedures was 6.0 days and intensive care unit (ICU) stay was 23.0h. Re-operation for haemorrhage occurred in 2.1% of all cases and deep sternal infection in 0.4% of all cases. Crude 30-day operative mortality was 3.6% for all procedures; 2.1% for isolated CABG, 3.6% for valve procedures, 5.2% for valve and CABG and 11.4% for other cardiac surgical procedures. Mortality rates increased from 1.8% for elective procedures to 4.1% for urgent and 24.6% for emergency or salvage operations. In comparison to international figures from the USA and UK, mortality rates following isolated CABG were lower whilst average length of hospital stay post-procedure was higher. CONCLUSION: The ASCTS database project is now well established and the electronic database and reporting module is in operation in all participating sites. The risk-adjusted isolated operative mortality suggests cardiac surgical performance in Victoria compares well with international standards. As the database develops, local risk-adjustment models for mortality and morbidity for each procedure will be developed to enable appropriate between hospital comparisons.

Journal Article↗
PubMedDate not supplied

Data quality assurance for thermophysical property databases--applications to the TRC SOURCE data system.

To a significant degree processes of database development are based upon human activities, which are susceptible to various errors. Propagation of errors in the processing leads to a decrease in the value of original data as well as that of any database products. Data quality is a critical issue that every database producer must handle as an inseparable part of the database management. Within the Thermodynamics Research Center (TRC), a systematic approach to implement database integrity rules was established through the use of modern database technology, statistical methods, and thermodynamic principles. The four major functions of the system--error prevention, database integrity enforcement, scientific data integrity protection, and database traceability--are detailed in this paper.

Journal Article↗
PubMed2007

The quality of reports of critical care meta-analyses in the Cochrane Database of Systematic Reviews: an independent appraisal.

OBJECTIVE: To independently appraise the methodological quality of a sample of reports of meta-analyses that address critical care topics in the Cochrane Database of Systematic Reviews compared with the quality of reports published in regular journals, using a validated assessment instrument, the Overview Quality Assessment Questionnaire (OQAQ). DATA SOURCE: Studies were selected from a search of MEDLINE, EMBASE, and the Cochrane Database of Systematic Reviews from 1994 to 2003, using multiple search terms for critical care and sensitive filters to identify meta-analyses. STUDY SELECTION: Two authors independently selected meta-analyses that addressed topics pertinent to critical care medicine. DATA EXTRACTION: Two authors independently extracted the data. The proportion of reports that met each component of the OQAQ was determined, as was the overall quality score. Meta-analyses published in the Cochrane Database of Systematic Reviews were compared with those published in regular journals. DATA SYNTHESIS: There were 36 reports of meta-analyses in the Cochrane Database of Systematic Reviews and 103 reports of meta-analyses published in regular journals; 11 of these were reports of Cochrane reviews. The meta-analyses published in the Cochrane Database of Systematic Reviews were more likely to fulfill most components of the OQAQ. The median overall OQAQ scores indicated significant methodological problems in the reports regardless of the source of publication, although the reports in the Cochrane database scored higher than those in regular journals (five compared with two, p<.001). Major methodological flaws, notably failure to appropriately refer to the validity of included studies, were found in meta-analyses in both the Cochrane Database of Systematic Reviews and regular journals (44.4% and 79.3%, respectively). CONCLUSIONS: Although the quality of reports of meta-analyses published in the Cochrane Database of Systematic Reviews is superior to the quality of reports of meta-analyses published in regular journals, there is significant room for improvement. Clinicians should critically appraise all reports of meta-analyses before considering the results, regardless of the source of publication.

Critical Care↗
PubMed2005

Los alamos hepatitis C immunology database.

The Los Alamos Hepatitis C Virus (HCV) Sequence Database (http://hcv.lanl.gov or http://hcv-db.org) was officially launched in September 2003. The sister HCV Immunology Database was made public in September 2004. The HCV Immunology Database is based on the Human Immunodeficiency Virus (HIV) Immunology Database. The HCV Immunology Database contains a curated inventory of immunological epitopes in HCV and their interaction with the immune system, with associated retrieval and analysis tools. This article describes in detail the types of data and services that the new database offers, the tools provided and the database framework. The data and some of the HCV database tools are available for download for non-commercial use.

Journal Article↗
PubMed1995

Delivering health information databases on World Wide Web at the National University of Singapore.

The National University of Singapore (NUS) is one of the first medical schools in Asia to exploit the use of the World Wide Web on the Internet for the delivery of health information databases. Its WWW server was established in 1993 by the NUS Biocomputing Research and User Support (BRUS) technology group in collaboration with the Computer Resource Planning committee of the Faculty of Medicine. As a result of the early recognition of the powerful platform on which health information services can be delivered worldwide, the NUS effort has been accredited with a number of Internet firsts in the area of health informatics. The following are some of the NUS achievements: NUS-NCI CancerNet on the Web. The NUS developed and implemented the first WWW version of the popular CancerNet database offered by the National Cancer Institute, NIH, USA. Health Info-Com Network Medical Newsletter. The NUS developed and implemented the first WWW version of the medical newsletter, MEDNEWS which is edited by Dr. David Dodell, USA. It is now mirrored by the University of Pennsylvania in the United States and De Montfort University, U.K. Poisons Information Database. This first WWW implementation of a database on known plant, snake and other animal toxins with directories of antivenoms, toxinologists and poisons control centers around the world is offered by the NUS Venom and Toxin Research Group. HistoNet. This is a large collection of histology specimens from the NUS Department of Anatomy. MEDISTAT. This is the first WWW implementation of a Health and Population Statistical Database which contains information for Singapore, selected Asian countries and aggregate data for world regions. The Singapore Biotechnology Database. This database features companies and organizations involved in biotechnology and related activities in Singapore. Efforts are continuing to offer more value-added health information databases on the NUS WWW server and to link the server with other top-class information centers worldwide. Our mission is to identify the National University of Singapore as a global health information hub on the Internet.

Computer Communication Networks↗
PubMedDate not supplied

Design and realization of an on-line database for multidimensional microscopic images of biological specimens.

The BioImage database is a new scientific database for multidimensional microscopic images of biological specimens, which is available through the World Wide Web (WWW). The development of this database has followed an iterative approach, in which requirements and functionality have been revised and extended. The complexity and innovative use of the data meant that technical and biological expertise has been crucial in the initial design of the data model. A controlled vocabulary was introduced to ensure data consistency. Pointers are used to reference information stored in other databases. The data model was built using InfoModeler as a database design tool. The database management system is the Informix Dynamic Server with Universal Data Option. This object-relational system allows the handling of complex data using features such as collection types, inheritance, and user-defined data types. Informix datablades are used to provide additional functionality: the Web Integration Option enables WWW access to the database; the Video Foundation Blade provides functionality for video handling.

Animals↗
PubMed2003

The UAB Proteomics Database.

SUMMARY: The University of Alabama at Birmingham (UAB) Proteomics Database (UPD) (http://www.uab.edu/proteinmenu) was created to provide a repository for the storage and linkage of two-dimensional (2D) gel images and the associated information obtained through mass spectrometry analysis of the proteins excised from the 2D gels in a manner similar to the SWISS-2DPAGE database and the Stanford Microarray Database. This was accomplished through the development of a web interface, a relational database, image maps and hyperlinks stored in the database. In addition to the internally generated data, UPD provides links to the National Center for Biotechnology Information via accession number hyperlinks. UPD currently contains information on 44 individual proteins derived from four experiments conducted by four UAB faculty members. Images of the gels from which each of these proteins was isolated are accessed by hyperlinks embedded in the database. AVAILABILITY: The UAB Proteomics Database can be accessed at http://www.uab.edu/proteinmenu.

Alabama↗
PubMed2002

YPL.db: the Yeast Protein Localization database.

The Yeast Protein Localization database (YPL.db) contains information about the localization patterns of yeast proteins resulting from microscopic analyses. The data and parameters of the experiments to obtain the localization information, together with images from confocal or video microscopy, are stored in a relational database, building an archive of, and the documentation for, all experiments. The database can be queried based on gene name, protein localization, growth conditions and a number of additional parameters. All experiment parameters are selectable from predefined lists to ensure database integrity and conformity across different investigators. The database provides a structure reference resource to allow for better characterization of unknown or ambiguous localization patterns. Links to MIPS, YPD and SGD databases are provided to allow fast access to further information not contained in the localization database itself. YPL.db is available at http://ypl.tugraz.at.

Computer Graphics↗
PubMed2002

Project IMPACT: results from a pilot validity study of a new observational database.

OBJECTIVE: The objective of this study was to evaluate the accuracy of the information contained in the Project IMPACT database. Project IMPACT is a comprehensive database system developed to measure and describe the care of intensive care patients. This database is being used by a large group of hospitals to help clinicians improve the care of these patients. Data on patient demographics, diagnoses, treatment, and outcomes are entered into the Project IMPACT database by staff at participating hospitals. This pilot study was a first step in assessing the accuracy of these data to determine the usefulness of the Project IMPACT database for measuring intensive care unit (ICU) performance and patient outcomes. DESIGN: The design of the pilot study was the independent abstraction of selected data items from a random sample of ICU patient records from two hospitals participating in Project IMPACT. The abstracted data were compared with the data existing in the Project IMPACT database for agreement. SETTING: Abstraction was performed onsite at the two pilot hospitals by a trained abstractor who was not affiliated with either hospital. PATIENTS: Patients whose records were abstracted included 45 randomly selected ICU patients at each of the two pilot hospitals. MEASUREMENTS AND MAIN RESULTS: Comparison of the Project IMPACT data with the independently abstracted data indicated good agreement (80% or above) on discrete items, such as type of ICU patient. Poorer agreement (under 80%) was seen for continuous items (e.g., 24-hr urine output) and coded items requiring judgment (e.g., reason for ICU admission). CONCLUSIONS: The pilot study showed good internal validity for most of the abstracted variables. High agreement rates were observed, regardless of method of original data capture (electronic download or manual entry), although agreement was higher for some data items that had been electronically downloaded into the Project IMPACT database. The results suggest that Project IMPACT is a valuable resource for ICUs to collect and evaluate information about treatment and patient outcomes.

Database Management Systems↗
PubMedDate not supplied

Temporal expressiveness in querying a time-stamp--based clinical database.

Most health care databases include time-stamped instant data as the only temporal representation of patient information. Many previous efforts have attempted to provide frameworks in which medical databases could be queried in relation to time. These, however, have required either a sophisticated database representation of time, including time intervals, or a time-stamp-based database coupled with a nonstandard temporal query language. In this work, the authors demonstrate how their previously described data retrieval application, DXtractor, can be used as a database querying application with expressive power close to that of temporal databases and temporal query languages, using only standard SQL and existing time-stamp-based repositories. DXtractor provides the ability to compose temporal queries through an interface that is understood by nonprogramming medical personnel. Not all temporal constructs are easily implemented using this framework; nonetheless, DXtractor's temporal capabilities provide a significant improvement in the temporal expressivity accessible to clinicians using standard time-stamped clinical databases.

Database Management Systems↗
PubMed2004

Lung image database consortium: developing a resource for the medical imaging research community.

To stimulate the advancement of computer-aided diagnostic (CAD) research for lung nodules in thoracic computed tomography (CT), the National Cancer Institute launched a cooperative effort known as the Lung Image Database Consortium (LIDC). The LIDC is composed of five academic institutions from across the United States that are working together to develop an image database that will serve as an international research resource for the development, training, and evaluation of CAD methods in the detection of lung nodules on CT scans. Prior to the collection of CT images and associated patient data, the LIDC has been engaged in a consensus process to identify, address, and resolve a host of challenging technical and clinical issues to provide a solid foundation for a scientifically robust database. These issues include the establishment of (a) a governing mission statement, (b) criteria to determine whether a CT scan is eligible for inclusion in the database, (c) an appropriate definition of the term qualifying nodule, (d) an appropriate definition of "truth" requirements, (e) a process model through which the database will be populated, and (f) a statistical framework to guide the application of assessment methods by users of the database. Through a consensus process in which careful planning and proper consideration of fundamental issues have been emphasized, the LIDC database is expected to provide a powerful resource for the medical imaging research community. This article is intended to share with the community the breadth and depth of these key issues.

Biomedical Research↗
PubMed2005

The Australian EEG database.

The Australian EEG Database is a web-based de-identified searchable database of 18,500 EEG records recorded at a regional public hospital over an 11-year period. Patients range in age from a premature infant born at 24 weeks gestation, through to people aged over 90 years. This paper will describe the history of the database, the range of patients represented in the database, and the nature of the text-based and digital data contained in the database. Preliminary results of the first two studies undertaken using the database are presented. Plans for sharing data from the Australian EEG database with researchers are discussed. We anticipate that such data will be useful in not only helping to answer clinical questions but also in the field of mathematical modeling of the EEG.

Adolescent↗
PubMed2006

A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila.

BACKGROUND: Biological processes are mediated by networks of interacting genes and proteins. Efforts to map and understand these networks are resulting in the proliferation of interaction data derived from both experimental and computational techniques for a number of organisms. The volume of this data combined with the variety of specific forms it can take has created a need for comprehensive databases that include all of the available data sets, and for exploration tools to facilitate data integration and analysis. One powerful paradigm for the navigation and analysis of interaction data is an interaction graph or map that represents proteins or genes as nodes linked by interactions. Several programs have been developed for graphical representation and analysis of interaction data, yet there remains a need for alternative programs that can provide casual users with rapid easy access to many existing and emerging data sets. DESCRIPTION: Here we describe a comprehensive database of Drosophila gene and protein interactions collected from a variety of sources, including low and high throughput screens, genetic interactions, and computational predictions. We also present a program for exploring multiple interaction data sets and for combining data from different sources. The program, referred to as the Interaction Map (IM) Browser, is a web-based application for searching and visualizing interaction data stored in a relational database system. Use of the application requires no downloads and minimal user configuration or training, thereby enabling rapid initial access to interaction data. IM Browser was designed to readily accommodate and integrate new types of interaction data as it becomes available. Moreover, all information associated with interaction measurements or predictions and the genes or proteins involved are accessible to the user. This allows combined searches and analyses based on either common or technique-specific attributes. The data can be visualized as an editable graph and all or part of the data can be downloaded for further analysis with other tools for specific applications. The database is available at http://proteome.wayne.edu/PIMdb.html CONCLUSION: The Drosophila Interactions Database described here places a variety of disparate data into one easily accessible location. The database has a simple structure that maintains all relevant information about how each interaction was determined. The IM Browser provides easy, complete access to this database and could readily be used to publish other sets of interaction data. By providing access to all of the available information from a variety of data types, the program will also facilitate advanced computational analyses.

Database Management Systems↗
PubMed2005

Bcipep: a database of B-cell epitopes.

BACKGROUND: Bcipep is a database of experimentally determined linear B-cell epitopes of varying immunogenicity collected from literature and other publicly available databases. RESULTS: The current version of Bcipep database contains 3031 entries that include 763 immunodominant, 1797 immunogenic and 471 null-immunogenic epitopes. It covers a wide range of pathogenic organisms like viruses, bacteria, protozoa, and fungi. The database provides a set of tools for the analysis and extraction of data that includes keyword search, peptide mapping and BLAST search. It also provides hyperlinks to various databases such as GenBank, PDB, SWISS-PROT and MHCBN. CONCLUSION: A comprehensive database of B-cell epitopes called Bcipep has been developed that covers information on epitopes from a wide range of pathogens. The Bcipep will be source of information for investigators involved in peptide-based vaccine design, disease diagnosis and research in allergy. It should also be a promising data source for the development and evaluation of methods for prediction of B-cell epitopes. The database is available at http://www.imtech.res.in/raghava/bcipep.

B-Lymphocytes↗
PubMed1999

Development of a radiopharmaceutical information database.

OBJECTIVE: This article describes the development of a radiopharmaceutical (RP) computer database. Development and implementation of the database and services provided are presented. METHODS: A commercial database program was used to develop the structure for a radiopharmaceutical information database (RID) and to classify interaction information into several categories. The database is accessible to a variety of users through a network server. RESULTS: Information entered into the RID may be accessed easily and rapidly. The RID provides a wide spectrum of information services to its customers. CONCLUSION: The RID described is the first attempt to develop a database capable of entry and retrieval of RP information in an efficient and timely manner. The database is easy to use and maintain, and has virtually unlimited storage space on a network drive.

Database Management Systems↗
PubMed2003

A protocol for the update of references to scientific literature in biological databases.

Entries in biological databases are usually linked to scientific references. To generate those links and to keep them up-to-date, database maintainers have to continuously scan the scientific literature to select references that are relevant for each single database entry. The continuous growth of both the corpus of scientific literature and the size of biological databases makes this task very hard. We present a protocol intended to assist the updating of an existing set of literature (abstract) links from a single database entry with new references. It consists of taking the set of MEDLINE neighbour references of the existing linked abstracts and evaluating their relevance according to the existing set of abstracts. To test the applicability of the algorithm, we did a simple benchmark of the system using the references associated with the entries of a protein domain database. Human experts found the references that the algorithm scored highly were more relevant to the database entry than those scored lowly, suggesting that the algorithm was useful.

Abstracting and Indexing↗