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PubMed1999

Validation of the University of Manchester Drug Misuse Database.

OBJECTIVE: The study was conducted to assess the validity and quality of data held by one of the UK regional drug misuse databases (DMD). DESIGN: The research was multi-centred and used retrospective analysis to assess the validity of data held on the database. SETTING: The Regional Database is managed at the University of Manchester Drug Misuse Research Unit and uses data returned by medical and non-medical services within the UK's former North Western Regional Health Authority. MATERIAL: The research was largely based on analysis of the reporting or non-reporting to DMD of 1526 presentations by drug users to four community drug teams (CDTs) during the course of 1993. Two datasets were used: the DMD dataset, based on returns to the regional database from the agencies in question; and agency client records. Additionally the data included on a random sample of 300 database forms returned by these CDTs were compared with information contained in client records. MAIN OUTCOME MEASURES: The study reports on how well DMD is functioning in relation to the correct reporting of episodes of problem drug use and the quality of data held. RESULTS: A very high level of agreement (0.875 +/- 0.017, 95% CI, kappa coefficient 0.728) was established between reports sent in to the database and those expected by examination of agency records. The database figures underestimated the total number of episodes that should have been reported by a factor of 0.008. It was also established that 0.906 (+/- 0.018, 95% CI) of the reports made to the database were made correctly, that 0.178 (+/- 0.030, 95% CI) of eligible presentations were not reported, and that 0.166 (+/- 0.030, 95% CI) of ineligible presentations were mistakenly reported. Lastly, it was established that data were unnecessarily missing or inaccurately recorded in 0.027 of cases and that data entry errors occurred in 0.015 of cases. CONCLUSIONS: The validation project showed that the DMD system is very reliable, providing accurate measures of the extent and nature of presenting problem drug use in the region under study.

Confidentiality↗
PubMed2004

A database for G proteins and their interaction with GPCRs.

BACKGROUND: G protein-coupled receptors (GPCRs) transduce signals from extracellular space into the cell, through their interaction with G proteins, which act as switches forming hetero-trimers composed of different subunits (alpha,beta,gamma). The alpha subunit of the G protein is responsible for the recognition of a given GPCR. Whereas specialised resources for GPCRs, and other groups of receptors, are already available, currently, there is no publicly available database focusing on G Proteins and containing information about their coupling specificity with their respective receptors. DESCRIPTION: gpDB is a publicly accessible G proteins/GPCRs relational database. Including species homologs, the database contains detailed information for 418 G protein monomers (272 Galpha, 87 Gbeta and 59 Ggamma) and 2782 GPCRs sequences belonging to families with known coupling to G proteins. The GPCRs and the G proteins are classified according to a hierarchy of different classes, families and sub-families, based on extensive literature searchs. The main innovation besides the classification of both G proteins and GPCRs is the relational model of the database, describing the known coupling specificity of the GPCRs to their respective alpha subunit of G proteins, a unique feature not available in any other database. There is full sequence information with cross-references to publicly available databases, references to the literature concerning the coupling specificity and the dimerization of GPCRs and the user may submit advanced queries for text search. Furthermore, we provide a pattern search tool, an interface for running BLAST against the database and interconnectivity with PRED-TMR, PRED-GPCR and TMRPres2D. CONCLUSIONS: The database will be very useful, for both experimentalists and bioinformaticians, for the study of G protein/GPCR interactions and for future development of predictive algorithms. It is available for academics, via a web browser at the URL: http://bioinformatics.biol.uoa.gr/gpDB.

Databases, Protein↗
PubMed2004

Recruitment of patients into an internet-based clinical trials database: the experience of OncoLink and the National Colorectal Cancer Research Alliance.

PURPOSE: In March 2001, the National Colorectal Cancer Research Alliance (NCCRA) and OncoLink (http://www.oncolink.org) established a database to facilitate patient enrollment onto clinical trials. This study describes the population registering with the database and identifies discrepancies between individuals registering through the Internet and those registering through a telephone call center. METHODS: Participants registered with the NCCRA/OncoLink database through the Internet or a telephone call center. All participants entering the database completed a questionnaire regarding basic demographics, colon cancer risk factors, and indicated how they became aware of the database. Comparisons were made between individuals registering through the Internet and those registering through the telephone call center. RESULTS: A total of 2,162 participants registered during the first 16 months of the database. Most patients registered through the Internet rather than the telephone call center (88% v 12%; P < .001). More females than males registered (73% v 27%; P < .001). The majority (89%) were white. Participants registering through the Internet were younger than those registering through the call center (mean, 48.8 v 55.0 years; P < .001). There was no difference between the two groups with regard to sex or ethnicity. CONCLUSION: The Internet has the potential to increase the likelihood that interested individuals find appropriate clinical trials. Some of the discrepancies that are known to exist for access to the Internet were also seen for those registering with the database through the Internet. Despite these differences, the potential to increase clinical trial enrollment with this type of Internet-based database is high.

Adolescent↗
PubMed2004

The dependence of all-atom statistical potentials on structural training database.

An accurate statistical energy function that is suitable for the prediction of protein structures of all classes should be independent of the structural database used for energy extraction. Here, two high-resolution, low-sequence-identity structural databases of 333 alpha-proteins and 271 beta-proteins were built for examining the database dependence of three all-atom statistical energy functions. They are RAPDF (residue-specific all-atom conditional probability discriminatory function), atomic KBP (atomic knowledge-based potential), and DFIRE (statistical potential based on distance-scaled finite ideal-gas reference state). These energy functions differ in the reference states used for energy derivation. The energy functions extracted from the different structural databases are used to select native structures from multiple decoys of 64 alpha-proteins and 28 beta-proteins. The performance in native structure selections indicates that the DFIRE-based energy function is mostly independent of the structural database whereas RAPDF and KBP have a significant dependence. The construction of two additional structural databases of alpha/beta and alpha + beta-proteins further confirmed the weak dependence of DFIRE on the structural databases of various structural classes. The possible source for the difference between the three all-atom statistical energy functions is that the physical reference state of ideal gas used in the DFIRE-based energy function is least dependent on the structural database.

Algorithms↗
PubMedDate not supplied

Evaluation of personal digital assistant drug information databases for the managed care pharmacist.

BACKGROUND: Personal digital assistants (PDAs) are becoming a necessity for practicing pharmacists. They offer a time-saving and convenient way to obtain current drug information. Several software companies now offer general drug information databases for use on hand held computers. PDAs priced less than 200 US dollars often have limited memory capacity; therefore, the user must choose from a growing list of general drug information database options in order to maximize utility without exceeding memory capacity. OBJECTIVE: This paper reviews the attributes of available general drug information software databases for the PDA. It provides information on the content, advantages, limitations, pricing, memory requirements, and accessibility of drug information software databases. SUMMARY: Ten drug information databases were subjectively analyzed and evaluated based on information from the product.s Web site, vendor Web sites, and from our experience. Some of these databases have attractive auxiliary features such as kinetics calculators, disease references, drug-drug and drug-herb interaction tools, and clinical guidelines, which may make them more useful to the PDA user. CONCLUSION: Not all drug information databases are equal with regard to content, author credentials, frequency of updates, and memory requirements. The user must therefore evaluate databases for completeness, currency, and cost effectiveness before purchase. In addition, consideration should be given to the ease of use and flexibility of individual programs.

Computers, Handheld↗
PubMed1991

A model for database design.

Computerized databases can facilitate several types of occupational therapy research. The value and usefulness of any database, however, is dependent on how well it has been designed. In this paper, a systematic, sequential-process model for the development of a computerized database is introduced. Each component of the model is illustrated by examples of its application to the actual design of a database for a community agency that provides occupational therapy services. The model focuses on issues related to the development of the contents of a database rather than on computer hardware and software. The issues addressed by the model include decisions about the purpose of the database, selection of the variables, and identification of the most appropriate measures with which to operationalize these variables. Content-related development issues have been given little attention in the literature, yet their neglect typically results in important limitations on the usefulness of a database. Therefore, this paper provides a set of guidelines for occupational therapists planning to establish a database for facilitating research.

Databases, Factual↗
PubMed1991

Search and find ... a PC database.

In this article on microcomputer databases, we will start off with a brief review of some common database terminology, specify some selection criteria, identify some common types of databases, and discuss some of the pros and cons of each. Two terms in usage with the classification of database software, flat-file versus a relational database, will also be explained. Then, I will share my personal use of each type of database, focusing in on an on-line Rolodex-type product to illustrate a canned, flat-file personal contacts database and a dedicated, programmable software program which can be used for unlimited relational database development.

Abstracting and Indexing↗
PubMedDate not supplied

Multiresidue screening of pesticides in foods using retention time locking, GC-AED, database search, and GC/MS identification.

Fruit and vegetable extracts were screened for over 400 pesticides by gas chromatography with atomic emission detection (GC-AED) and an experimental database. A technique called retention time locking was used to match GC-AED and GC with mass spectrometry (MS) retention times to those of the database. Samples were analyzed for sulfur, nitrogen, phosphorus, and chlorine by GC-AED. Possible pesticides were suggested by database search and identified by GC/MS. Forty-four pesticide standards were analyzed to determine the precision of retention time matching and the accuracy of the database search. Analytical retention times matched database retention times within 0.32 min. Using elemental criteria, the database search identified the correct compound for 41 of 44 pesticide standards. For blind spikes of fruit and vegetable extracts, the database suggested 22 of 26 spiked pesticides as matches. Nineteen were identified by GC/MS. The combination of retention time locking, GC-AED, database search, and GC/MS can be a powerful tool for identifying pesticides in a complex matrix.

Chlorine↗
PubMed2001

SWISS-PROT: connecting biomolecular knowledge via a protein database.

With the explosive growth of biological data, the development of new means of data storage was needed. More and more often biological information is no longer published in the conventional way via a publication in a scientific journal, but only deposited into a database. In the last two decades these databases have become essential tools for researchers in biological sciences. Biological databases can be classified according to the type of information they contain. There are basically three types of sequence-related databases (nucleic acid sequences, protein sequences and protein tertiary structures) as well as various specialized data collections. It is important to provide the users of biomolecular databases with a degree of integration between these databases as by nature all of these databases are connected in a scientific sense and each one of them is an important piece to biological complexity. In this review we will highlight our effort in connecting biological information as demonstrated in the SWISS-PROT protein database.

Amino Acid Sequence↗
PubMed2002

Developing, evaluating and maintaining a standardized stormwater BMP effectiveness database.

The Urban Water Resources Research Council of the American Society of Civil Engineers, under a cooperative agreement with the US Environmental Protection Agency, released Version 1.0 of the National Stormwater Best Management Practices (BMP) Database to the stormwater management community in 1999. The product included a loaded database of 71 BMPs, as well as data entry software for standardized reporting of BMP test data. In conjunction with the database, the project team developed BMP performance evaluation protocols and applied them to the data contained in the initial database. Since the initial database release, 42 new BMP data sets have been added to the database, which is now accessible via the Internet at www.bmpdatabase.org along with associated data evaluation reports and other project documentation. A national stormwater BMP data clearinghouse continues to screen and post new BMP data to the database, as well as respond to inquiries from the public. An overview of both of the database software and results of the data evaluation are provided in this paper.

Databases, Factual↗
PubMed2003

[Establishment of minimum medical geographic information systems database in China].

OBJECTIVE: To establish a minimum medical geographic information systems (GIS) database as a spatial decision supporting system (SDSS), and to use the database into public health practice in China. METHODS: Spatial data collected from different sources were standardized as decimal degree format, including: (1) satellite images covering areas of China; (2) digital maps of China in vector files; (3) diseases database and relevant models. RESULTS: Necessary satellite images for the database have been collected from NOAA AVHRR, Landsat TM, etc., including the normalized difference vegetation index (NDVI) images from AVHRR, earth surface temperature images from AVHRR, GTOPO30 DEM images from USGS and landuse images from USGS. The digital vector files for GIS analysis were collected including political (county, provinces, country) boundaries file, environmental (drainage, land cover, soil type) vector file, population data and climate data; Data on diseases mainly generated from survey or case reporting. Relevant models on transmission of Schistosoma japonicum and Plasmodium vivax, and models of Oncomelania hupensis and Anophores sinansis were developed, and the relevant environmental factors related to incidence of cancers were mapped, to test and verify those database. CONCLUSION: The database unified the data from different sources for users. Minimum medical data included in the database could be used in the practice of public health. It is expected that this database be used in a wider range.

Animals↗
PubMed2004

Novel retinal genes discovered by mining the mouse embryonic RetinalExpress database.

PURPOSE: Bioinformatics has emerged as a powerful tool for identifying novel genes and pathways associated with retinal biology and disease. The developing mouse retina expresses an exceedingly large and complex variety of genes. Many of these genes have not been characterized but nevertheless are likely to have important developmental or physiological functions. The purpose of this study was to use an in silico approach with a mouse embryonic retinal database of cDNAs/expressed sequence tags (ESTs) named RetinalExpress to identify previously uncharacterized genes that are represented in the developing retina. METHODS: cDNA clones unique to the RetinalExpress database were identified by comparing clones in the RetinalExpress database with those in other cDNA/EST databases. We used a hierarchical filtering procedure with high stringency criteria that included sequence quality, colinearity with hypothetical gene sequences, and absence of any substantial existing annotation to select clones that were likely to represent novel genes. Selected clones were located on mouse chromosomes using National Center for Biotechnology Informatics Map Viewer software and the database from the University of California at Santa Cruz Genome Bioinformatics Web browser. The expression of selected retinal transcripts was determined using reverse transcriptase (RT)-PCR. In situ hybridization of sectioned embryonic and postnatal retinas was performed to determine spatial expression patterns of selected transcripts. RESULTS: Of the 27,765 cDNA clones from RetinalExpress that we filtered through several public cDNA/EST databases, 26 cDNA/EST sequences were identified that, at the time of the analysis, were unique to RetinalExpress. Seventeen clones were selected for RT-PCR analysis, and retinal transcripts corresponding to previously uncharacterized genes were unambiguously detected for six clones. Three genes encoded open reading frames containing putative functional domains; one sequence contained an HMG DNA binding domain, another, an RFX DNA binding domain, and another, a phospholipase C catalytic domain X. Transcripts from the genes encoding DNA binding domains were expressed in embryonic and postnatal retinas with distinct spatial patterns. CONCLUSIONS: The characterization of 26 mouse genes whose partial nucleotide sequences were uniquely represented in the RetinalExpress cDNA/EST database demonstrated the feasibility of retinal gene discovery using in silico analysis. Two of these genes had distinctive spatial expression patterns in the retina and one was likely to function as a DNA binding protein in embryonic and postnatal retinas. The gene identification approach described here demonstrates the usefulness of establishing large cDNA/EST databases from highly specialized neuronal tissues such as the retina to find novel genes.

Animals↗
PubMedDate not supplied

The CORRONA database.

BACKGROUND: Large, long-term databases are needed in order to provide information on the safety and efficacy of new agents used in the treatment of rheumatoid arthritis (RA) and psoriatic arthritis (PsA). These databases can provide data which is well beyond what is available from industry-sponsored investigations. METHODS: The structure, governance, content, context and developmental plan of the CORRONA database is described. RESULTS: The CORRONA database has grown from start up in 2002 to the largest independent database in North America which collects data from both rheumatologists and patients at the time of a clinical encounter. Data are collected as often as every 3 months in RA and every 6 months in PsA. As of the time of this writing, the CORRONA database consists of approximately 9,000 patients with RA and 1,000 with PsA. Data can be used to elucidate toxicities found in frequencies which would be considerably less common than can be uncovered in industry-sponsored investigations. In addition, actual prescribing patterns and responses in clinical practice can be investigated and described. CONCLUSION: After 3 years of data collection, the CORRONA database is now appropriately able to make significant contributions to our understanding of the safety, efficacy of drugs, as well as demographic, and socioeconomic profiles of patients with RA and PsA. It has evolved from a nascent database to a mature one poised to make significant contributions.

Antirheumatic Agents↗
PubMed2006

Searching for evidence in pediatric occupational therapy using free versus subscription databases: a comparison of outcomes.

OBJECTIVE: This study compared the results of searching free versus subscription databases and using brief versus comprehensive search strategies to locate evidence for three pediatric occupational therapy clinical questions. METHOD: Three clinical questions were nominated by practicing pediatric occupational therapists. Brief and comprehensive search strategies were then developed. Searches were conducted in three free-to-access databases and four subscription databases. RESULTS: Based on descriptive data, more relevant citations were retrieved using the subscription databases compared with the free databases and when using a comprehensive search strategy. Citations that were present in some databases were not always retrieved by the searches. This was mainly due to the inclusion of an insufficient number of search terms in the brief search strategies used in this study and a mismatch between terms used in the search strategies and the databases. CONCLUSION: Clinicians may need to use both subscription and free databases and use comprehensive search strategies to maximize retrieval of relevant articles to answer pediatric clinical questions.

Australia↗
PubMed1994

Toward unification of taxonomy databases in a distributed computer environment.

All the taxonomy databases constructed with the DNA databases of the international DNA data banks are powerful electronic dictionaries which aid in biological research by computer. The taxonomy databases are, however not consistently unified with a relational format. If we can achieve consistent unification of the taxonomy databases, it will be useful in comparing many research results, and investigating future research directions from existent research results. In particular, it will be useful in comparing relationships between phylogenetic trees inferred from molecular data and those constructed from morphological data. The goal of the present study is to unify the existent taxonomy databases and eliminate inconsistencies (errors) that are present in them. Inconsistencies occur particularly in the restructuring of the existent taxonomy databases, since classification rules for constructing the taxonomy have rapidly changed with biological advancements. A repair system is needed to remove inconsistencies in each data bank and mismatches among data banks. This paper describes a new methodology for removing both inconsistencies and mismatches from the databases on a distributed computer environment. The methodology is implemented in a relational database management system, SYBASE.

Animals↗
PubMed1994

Obstacles and approaches to clinical database research: experience at the University of California, San Francisco.

With increasing availability of clinical data in machine-readable form, and decreasing cost of storing and manipulating that data, retrospective research using clinical databases has become more feasible. Nonetheless, much of the potential for clinical research using these data remains unrealized. Obstacles to clinical database research include difficulty accessing data, difficulty using retrospective data to draw valid inferences about medical tests and treatments, and a shortage of investigators trained and interested in using a clinical database to answer their questions. At the University of California, San Francisco, we have developed a Clinical Database Research Program (CDRP) to try to overcome these obstacles. The CDRP maintains a relational database of patient data obtained from diverse sources and a small staff dedicated to providing such data to researchers. The CDRP staff also provides support for design and analysis of studies using the database--the development of methods for such studies is our primary research interest. Finally, to increase the number of investigators using the database for research, we are integrating training in clinical epidemiology and clinical research methods into residency and fellowship training, and offering an elective in clinical database research for trainees who wish to undertake a specific project.

Databases, Factual↗
PubMed1996

A survey of population-based drug databases in Canada.

OBJECTIVE: To identify the population-based drug databases in Canada and to determine their comprehensiveness and accessibility for performing pharmacoepidemiologic and outcomes research. DESIGN: Survey (four-part mailed questionnaire). SETTING: Public and private third-party drug plans across Canada. PARTICIPANTS: All provincial and territorial drug plan or pharmacare managers as well as selected private plan managers including health benefit consultants, group insurers and claims adjudicators/pharmacy benefit managers (CA/PBMs). OUTCOME MEASURES: Patient, drug and pharmacy information; potential for electronic linkages to other provincial databases (e.g., physician, hospital, vital statistics); accessibility of information; population profile. RESULTS: Of the 32 recipients of the questionnaire 29 (91%) responded and 18 (56%) completed the survey. Most databases were reported to contain patient information (e.g., patient identification number, age, sex and medication history) and prescription drug information (e.g., drug identification number, strength, quantity and cost). Six provinces and one territory reported the capability to link to other databases (e.g., hospital and physician databases). One CA/PBM reported some links to selected long-term disability data. All of the government databases except those in British Columbia and the Yukon Territory allowed use of the data for research purposes. Manitoba and Saskatchewan included all residents of the province in their database; the others included selected groups (e.g., residents 65 years of age or older, people on social assistance or people covered by private group insurance). CONCLUSION: A number of public and private population-based databases are available for use in pharmacoepidemiologic and outcomes research.

Canada↗
PubMed1996

Database and knowledge base integration--a data mapping method for Arden Syntax knowledge modules.

One of the most important categories of decision-support systems in medicine are data driven systems where the inference engine is linked to a database. It is, therefore, important to find methods that facilitate the implementation of database queries referred to in the knowledge modules. A method is described for linking clinical databases to a knowledge base with Arden Syntax modules. The method is based on a query meta-database including templates for SQL queries which is maintained by a database administrator. During knowledge module authoring the medical expert refers only to a code in the query meta-database; no knowledge is needed about the database model or the naming of attributes and relations. The method uses standard tools, such as C+2 and ODBC, which makes it possible to implement the method at many platforms and to link to different clinical databases in a standardized way.

Databases, Factual↗