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PubMed2002

A comparison of technologies for database-driven websites for medical education.

Static web pages may be easy to setup using text processors or user-friendly web editing software. However, some basic knowledge of the implementation (HTML) is usually needed for final editing and maintenance. As a result many static web pages are left without appropriate updating. With a database driven, dynamic approach web contents may change through user interaction, the pages are usually easier to maintain, and design elements are separated from contents. Database driven solutions (or content management systems) for larger organizations may be purchased at many different levels of complexity. For smaller systems, such as separate courses or projects, they may, however, be developed locally. The present study compares four alternative technologies for database driven web pages. Each technology offers advantages and disadvantages and many issues need to be considered when selecting platform. The present study demonstrates that database driven web pages may be effectively deployed using free Open Source software. Details may be found at www.intermed.dk/datadriven.

Computer User Training↗
PubMed2004

Building an organ-specific carcinogenic database for SAR analyses.

FDA reviewers need a means to rapidly predict organ-specific carcinogenicity to aid in evaluating new chemicals submitted for approval. This research addressed the building of a database to use in developing a predictive model for such an application based on structure-activity relationships (SAR). The Internet availability of the Carcinogenic Potency Database (CPDB) provided a solid foundation on which to base such a model. The addition of molecular structures to the CPDB provided the extra ingredient necessary for SAR analyses. However, the CPDB had to be compressed from a multirecord to a single record per chemical database; multiple records representing each gender, species, route of administration, and organ-specific toxicity had to be summarized into a single record for each study. Multiple studies on a single chemical had to be further reduced based on a hierarchical scheme. Structural cleanup involved removal of all chemicals that would impede the accurate generation of SAR type descriptors from commercial software programs; that is, inorganic chemicals, mixtures, and organometallics were removed. Counterions such as Na, K, sulfates, hydrates, and salts were also removed for structural consistency. Structural modification sometimes resulted in duplicate records that also had to be reduced to a single record based on the hierarchical scheme. The modified database containing 999 chemicals was evaluated for liver-specific carcinogenicity using a variety of analysis techniques. These preliminary analyses all yielded approximately the same results with an overall predictability of about 63%, which was comprised of a sensitivity of about 30% and a specificity of about 77%.

Animals↗
PubMed2002

Development of a Chinese herbal medicine toxicology database.

BACKGROUND: Use of Chinese herbal medicine has increased steadily in the West and adverse reactions have been reported. However, information is not readily available on the toxicity of the herbs and the management of poisoning. The goals of this project were to retrieve and evaluate scientific evidence on the toxicity of Chinese herbal medicine, to grade the toxicity of individual herbs, and to summarize relevant herb data via a searchable electronic database. METHODS: English and Chinese primary studies were systematically retrieved via journal abstracting databases and key toxicity texts. Partial translation of published research was achieved via an audited process utilizing data extraction forms. Methods for grading herb toxicity (in therapeutic use or overdose) were developed based on a combination of the quality of reports, severity of adverse reaction, supporting animal studies, extrapolation from pharmacology and empirical evidence. RESULTS: Good quality studies on the toxicity of Chinese herbs are lacking. In some cases there is insufficient scientific evidence to create an evidence-based grading of the toxicity of individual herbs. Available data have been summarized into detailed monographs. Twelve herb monographs (with a full toxicity profile and grading) have been completed and summary data for all adequate quality papers used in the grading are linked to the monographs. CONCLUSIONS: The resultant database and monographs represent the first reviews specifically on the toxicity of individual Chinese herbs with toxicological grades based on the evidence of published studies. The database and monographs should assist in promoting the safe and effective use of Chinese herbal medicine.

Databases, Factual↗
PubMed2002

TLFAM--a new set of protein family databases.

PFAM is a popular and effective database of Hidden Markov Models (HMMs), which represent a wide range of protein families. Here, we introduce TLFAM as a more specific set of HMM databases. Analyses of bacterial genomes using TLFAM-Pro show better scores, E-values, and alignment lengths than those using the more generalized PFAM. Since PFAM will still find hits that TLFAM-Pro will not, we recommend that they be used jointly, rather than exclusively. This method provides the best features of both databases. This method has been extended to a number of other organism types, such as archaea, and the databases are freely available to interested researchers.

Databases, Protein↗
PubMed1997

Directory of Databases for research into alternative and complementary medicine.

This Directory of Databases with significant holdings of primarily bibliographic references to complementary and alternative medicine research resources has been compiled to facilitate access to the widely scattered data and literature. The Directory is directly accessible from the Web site of the Richard & Hinda Rosenthal Center for Complementary and Alternative Medicine at Columbia University's CPMCNet (http://cpmcnet.columbia.edu/dept/rosenthal/). General selection criteria and a brief description of content, access, or contact details are given for each of the 56 databases. Thirty-five of the databases are available online over the Internet and of these, 17 are freely, publicly available. There are 13 search services and a further 8 databases available in a variety of formats.

Complementary Therapies↗
PubMed1997

Directory of databases for research into alternative and complementary medicine: an update.

The Directory of Databases with significant holdings of primarily bibliographic references to complementary and alternative medicine research resources has been compiled to facilitate access to the widely scattered data and literature. The Directory is directly accessible from the Web site of the Richard & Hinda Rosenthal Center for Complementary and Alternative Medicine at Columbia University's CPMCNet (http:/(/)cpmcnet.columbia.edu/dept/rosenthal/) where it is kept regularly updated. General selection criteria and a brief description of content, access or contact details are given for each of the 56 databases. Thirty-six of the databases are available online over the Internet and of these, 17 are freely, publicly available. There are 13 search services and a further 8 databases available in a variety of formats. Following are some recent updates to supplement the written version of the Directory published in this journal (Wootton, 1997). The section numbering corresponds to the numbering in the original article and on the Columbia University Web site.

Complementary Therapies↗
PubMed2005

AKA-Glucose: a program for kinetic and epidemiological analysis of frequently sampled intravenous glucose tolerance test data using database technology.

BACKGROUND: The Bergman Minimal Model enables estimation of two key indices of glucose/ insulin dynamics: glucose effectiveness and insulin sensitivity. METHODS AND RESULTS: In this paper we describe AKA-Glucose, a program that combines MINMOD Millennium (minimal model analysis software) with relational database technologies. AKA-Glucose enables the fitting of individual frequently sampled intravenous glucose tolerance test (FSIGT) data sets to the Minimal Model and the secure storage in a dedicated database (and retrieval from) of thousands of individual subjects' demographic data, their individual FSIGT data, and each subject's parameters and indices derived from minimal model analysis. AKA-Glucose also enables the population analysis of various strata or subpopulations within the database. AKA-Glucose has all of the capabilities of MINMOD Millennium, provides Minimal Model parameter estimates that are concordant with estimates from previous MINMOD software, and allows importation of data files from earlier versions of the MINMOD software. CONCLUSIONS: By combining FSIGT data fitting, population analysis, and relational database technologies, AKA-Glucose is the first minimal model software designed specifically for researchers confronted with minimal model and epidemiological analysis of large numbers of either human or animal FSIGT data sets.

Adult↗
PubMed2004

Prototype database for telerehabilitation.

Telerehabilitation is a promising alternative health-care delivery system, but currently lacks broad-based empirical support for the efficacy and cost utility of its interventions. This article describes the development of a database at INTEGRIS Jim Thorpe Rehabilitation Center (IJTRC) that will link the delivery of telerehabilitation services, reimbursement, and outcomes evaluation. The database is a culmination of the combined efforts of administrators, clinicians, and information technology professionals. Feasibility of the project was first established from technical, economic, and organizational perspectives. The current workflow and documentation processes were analyzed and enhanced. This was followed by data modeling and design of the database architecture in terms of network, security, scalability, and system specification. A prototype was created in Microsoft Access with the final product planned in Structured Query Language (SQL) with a front-end in JAVA JSP. The initial results with the database have been encouraging in terms of increased efficacy and security, process streamlining, error reduction, and collection of comprehensive standardized data for statistical analysis of clinical and research outcomes.

Databases as Topic↗
PubMed2000

Selection of control groups by using a commercial database and random digit dialing.

Identifying a control group when cases come from a specialized hospital is a challenge for epidemiologists. The authors compared controls recruited by using a commercial database with those recruited by random digit dialing in the context of a hospital-based case-control study of ovarian cancer. This part of the study was conducted in 1997-1998 among women aged 18 years or older who resided in the New York metropolitan area. A mailing list owner grouped cases into "lifestyle" clusters based on US zip+4 postal code microneighborhoods and generated a random sample of potential controls with the same distribution across the clusters. Controls recruited from the commercial database (n = 82) and from random digit dialing (n = 90) were similar in age and race. Women from the commercial database had somewhat more education and higher incomes and were more similar to the cases on these measures. The control groups resembled each other closely in terms of oral contraceptive use, nulliparity, and religion and differed from the cases on these measures. Response rates were similar for the two groups. Only 28% of the cases were included on the mailing list, indicating that it did not reflect the source population of the cases. Use of a commercial database provided a control group whose socioeconomic factors were similar to those of cases at a lower cost than when random digit dialing was used but did not result in a higher response rate.

Adult↗
PubMed2002

Agreement on nutrient intake between the databases of the First National Health and Nutrition Examination Survey and the ESHA Food Processor.

The objective of this study was to assess agreement on nutrient intake between the nutrient database of the First National Health and Nutrition Examination Survey (NHANES I) and an up-to-date (December 1998) nutrient database, the ESHA Food Processor. Analysis was conducted among 11,303 NHANES I participants aged 25-74 years in 1971-1975 who had undergone dietary assessment. A list of all unique foods consumed was obtained from a single 24-hour dietary recall questionnaire administered during the baseline NHANES I visit. Foods on the list were matched to foods in the ESHA Food Processor software. Agreement between participants' nutrient intakes as calculated with the NHANES I and ESHA nutrient databases was assessed using intraclass correlation analysis, linear regression analysis, and graphic methods. Intraclass correlation analysis demonstrated excellent concordance between most nutrient intakes, with coefficients above 0.95 for intakes of energy, carbohydrates, protein, cholesterol, and calcium; coefficients between 0.90 and 0.95 for intakes of total fat, saturated fat, potassium, and vitamin C; and coefficients of approximately 0.85 for intakes of sodium and vitamin A. Graphic methods and regression analyses also showed good-to-excellent correspondence for most nutrients. These findings support the validity of expanding existing nutrient intake databases to explore current hypotheses, provided that food formulation, enrichment, and fortification practices have not changed substantially over time.

Adult↗
PubMed2006

Occupational exposure to mineral fibres: analysis of results stored on colchic database.

The aim of this paper is to present fibre exposure data recorded on the COLCHIC database. This database consolidates all occupational exposure data collected in French companies by the Caisses Régionales d'Assurance Maladie (regional health insurance funds, CRAM) and the Institut National de Recherche et de Sécurité (national institute for research and safety, INRS). A total of 8029 concentration results, expressed in number of fibres measured by phase-contrast optical microscopy, are available for exposure to asbestos fibres, ceramic fibres and man-made mineral fibres other than ceramic fibres. Presentation of base data by activity branch, activity sector or workplace permits identification of situations, for which prevention efforts are most essential. Analysis of exposure levels during the 1986-2004 period show that these are broadly influenced by changes in the exposure limit values. Wearing of respiratory protection equipment by employees is also discussed. The data may be helpful to occupational physicians performing occupational screening of exposed workers and to epidemiologists seeking information for building job-exposures matrices. In this respect, a database (FIBREX) will be available on the INRS web site (www.inrs.fr) at the beginning of 2007. This database will provide a higher level of detail in activity and workplace description than that which was possible for practical reasons in this paper.

Air Pollutants, Occupational↗
PubMed1995

MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices.

The information matrix database (IMD), a database of weight matrices of transcription factor binding sites, is developed. MATRIX SEARCH, a program which can find potential transcription factor binding sites in DNA sequences using the IMD database, is also developed and accompanies the IMD database. MATRIX SEARCH adopts a user interface very similar to that of the SIGNAL SCAN program. MATRIX SEARCH allows the user to search an input sequence with the IMD automatically, to visualize the matrix representations of sites for particular factors, and to retrieve journal citations. The source code for MATRIX SEARCH is in the 'C' language, and the program is available for unix platforms.

Base Sequence↗
PubMed1996

SIGNAL SCAN 4.0: additional databases and sequence formats.

SIGNAL SCAN is a program that utilizes transcription factor databases to find potential transcription factor binding sites in DNA sequences. The program is now in its fourth version. SIGNAL SCAN 4 now includes, in addition to the Transcription Factor Database, the TRANSFAC and IMD (Information Matrix Database) databases. In addition, it now accepts GCG and FASTA formatted DNA sequences in addition to Staden formatted sequences. SIGNAL SCAN is available for both IBM-compatible PC and Unix workstation platforms.

Binding Sites↗
PubMed1997

Using explicitly represented biological relationships for database navigation and searching via the World-Wide Web.

MOTIVATION: The increasing availability of biological databases on the World-Wide Web and hypertext links between them has made a wealth of information easily accessible to biologists. Additional retrieval capabilities can be achieved by storing explicitly specified biological relationships between different entities as discrete database entries. RESULTS: We have built CySPID, a prototype database about the cytoskeleton that explores the approach of explicitly representing biological relationships. The stored relationships are displayed along with other retrieved information, can be used to make hyperlinks to related entities, and can be used to search for entities with specified properties. CySPID is extensible in that new types of relationships may be created without altering the database schema. AVAILABILITY: CySPID is available for public use (http://ycmi.med.yale.edu/cyspid/). The CGI scripts used by CySPID are available upon request.

Animals↗
PubMed1998

An Internet linkage and mutation database for the complex phenotype asthma.

SUMMARY: The paper presents details of database construction, website installation and server architecture of the asthma and allergy gene database. AVAILABILITY: Database and server templates are available on request from the first author. SUPPLEMENTARY INFORMATION: The URL of the asthma and allergy gene database is http://cooke.gsf.de

Asthma↗
PubMed1999

MUTbase: maintenance and analysis of distributed mutation databases.

MOTIVATION: To develop tools for the submission of mutations to databases and maintenance of locus-specific mutation databases. Advanced, integrated computer systems are needed to store and organize the increasing mutation information. RESULTS: The MUTbase program suite provides an easy, interactive and quality-controlled submission of information to mutation databases. For further study of the databases on the World Wide Web, a number of tools are provided. The program package also writes and updates a large number of Web pages, e.g. about the distribution and statistics of disease-causing mutations, and changes in restriction patterns.

Algorithms↗
PubMed1999

Establishing a method of vector contamination identification in database sequences.

MOTIVATION: The nucleotide sequence databases are invaluable tools both for the private and the academic research communities, from the retrieval of sequences to homology searching. Several issues related to data quality, such as the existence of sequencing artifacts and errors, are facing the databases. We investigated a major source of these errors, i.e. the presence of vector-contaminated sequences. RESULTS: Using a panel of 180 vector polylinker sequences, we found 0.36% or 3029 vector-matching sequences in GenBank Release 95-96, with an average vector-matching length of 72 nucleotides. The number of vector-contaminated sequences has been growing with the database; however, the percent contamination has remained approximately constant at an average of 0.28% from 1982 to 1996. AVAILABILITY: Access to the database of vector polylinker sequences via sequence similarity searching is available at http://seqsim.ncgr.org/vector/ CONTACT: gas@molinfo.com

Animals↗
PubMed1999

KIND-a non-redundant protein database.

SUMMARY: KIND (Karolinska Institutet Nonredundant Database) is a protein database where identical sequences, both full length and partial, have been removed. The database contains nearly 274 900 sequences, half of which originate from the protein sequence databases Swissprot and PIR, while the other half come from translated open reading frames in GenPept and TrEMBL. AVAILABILITY: KIND is downloadable from ftp://ftp.mbb.ki.se/pub/KIND.

Algorithms↗