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PubMed1997

Databases and software for the analysis of mutations in the human p53 gene, the human hprt gene and both the lacI and lacZ gene in transgenic rodents.

We have created databases and software applications for the analysis of DNA mutations at the humanp53gene, the humanhprtgene and both the rodent transgeniclacIandlacZlocus. The databases themselves are stand-alone dBASE files and the software for analysis of the databases runs on IBM-compatible computers. Each database has a separate software analysis program. The software created for these databases permit the filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web (WWW). Open the following home page with a Web Browser: http://sunsite.unc.edu/dnam/mainpage.ht ml . Alternatively, the databases and programs are available via public FTP from: anonymous@sunsite.unc.edu . There is no password required to enter the system. The databases and software are found beneath the subdirectory: pub/academic/biology/dna-mutations. Two other programs are available at the site-a program for comparison of mutational spectra and a program for entry of mutational data into a relational database.

Animals↗

PubMed1998

Databases and software for the analysis of mutations in the human p53 gene, human hprt gene and both the lacI and lacZ gene in transgenic rodents.

We have created databases and software applications for the analysis of DNA mutations at the human p53 gene, the human hprt gene and both the rodent transgenic lacI and lacZ loci. The databases themselves are stand-alone dBASE files and the software for analysis of the databases runs on IBM-compatible computers with Microsoft Windows. Each database has a separate software analysis program. The software created for these databases permit the filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web. Open the following home page with a Web Browser: http://sunsite.unc.edu/dnam/mainpage. html . Alternatively, the databases and programs are available via public FTP from: anonymous@sunsite.unc.edu. There is no password required to enter the system. The databases and software are found beneath the subdirectory: pub/academic/biology/dna-mutations. Two other programs are available at the site, a program for comparison of mutational spectra and a program for entry of mutational data into a relational database.

Animals↗

PubMed1999

MIPS: a database for genomes and protein sequences.

The Munich Information Center for Protein Sequences (MIPS-GSF), Martinsried near Munich, Germany, develops and maintains genome oriented databases. It is commonplace that the amount of sequence data available increases rapidly, but not the capacity of qualified manual annotation at the sequence databases. Therefore, our strategy aims to cope with the data stream by the comprehensive application of analysis tools to sequences of complete genomes, the systematic classification of protein sequences and the active support of sequence analysis and functional genomics projects. This report describes the systematic and up-to-date analysis of genomes (PEDANT), a comprehensive database of the yeast genome (MYGD), a database reflecting the progress in sequencing the Arabidopsis thaliana genome (MATD), the database of assembled, annotated human EST clusters (MEST), and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). MIPS provides access through its WWW server (http://www.mips.biochem.mpg.de) to a spectrum of generic databases, including the above mentioned as well as a database of protein families (PROTFAM), the MITOP database, and the all-against-all FASTA database.

Amino Acid Sequence↗

PubMed2001

Accuracy of administrative and trauma registry databases.

OBJECTIVE: Accurate data are needed to evaluate clinical outcomes, therapeutic modalities, and quality of care in trauma. Administrative data, usually used for billing, and trauma registries, have been used to perform these functions. This study compares data for trauma patients from administrative and trauma registry databases at a Level I trauma center. METHODS: Data from patients injured in 1998 were obtained from both the trauma registry and administrative database. These International Classification of Diseases, Ninth Revision, Clinical Modification codes signify an admitting diagnosis of trauma. Patients from each database were "matched" by admission date, medical record number, age, and name. The two matched data sets were compared for accuracy in recording data. Chi-square analysis was used to compare groups. RESULTS: There were 2,702 patients found in both databases. One hundred eighteen patients with significant trauma were recorded in the trauma registry, but not in the administrative database. Comparison of recorded data for "matched" patients is as follows. The underreporting of mechanism of injury, diagnoses, diagnostic interventions, surgical procedures, and complications was rampant throughout the administrative database. Statistical significance was seen in the comparison between the trauma registry and the administrative database with motor vehicle collisions (458 vs. 391), abdominal injuries (346 vs. 293), orthopedic injuries (1,243 vs. 1,101), and thoracic injuries (486 vs. 397). Diagnostic interventions such as diagnostic peritoneal lavage, head computed tomographic scans, and abdominal computed tomographic scans were all grossly underrecorded, with only 40%, 12%, and 9% captured by the administrative database, respectively. Analysis of surgical procedures revealed these same trends, with statistical significance seen in abdominal and orthopedic procedures. Complications such as acute respiratory distress syndrome and deep venous thrombosis showed statistically significant differences. Mortality was underreported in the administrative database, with 14 deaths omitted. CONCLUSION: This study shows that administrative data have copious omissions of specific injuries, diagnostic and therapeutic interventions, as well as complications. The trauma registry recorded more of the diagnoses, diagnostics, procedures, and outcomes in the care of trauma patients. Trauma registries may be more useful than administrative databases in assessing quality of care and diagnostic and therapeutic interventions.

Adult↗

PubMed1992

The Jepson Lecture 1991. Clinical databases and surgical research.

Modern science is preoccupied with basic mechanisms at the level of the gene, molecule, atom and fundamental particle. This preoccupation has affected attitudes to medical science. Paradoxically, politicians and Departments of Health are largely concerned with clinical epiphenomena--outcomes, interventions, effectiveness, efficiency--that are often disregarded by medical scientists and viewed without favour by granting bodies. In the surgical sciences, there is renewed interest in clinical research. The small computer and the readily available database with its compatible statistical package have added a new dimension to clinical research. Database design and analysis are as much a part of the surgical investigator's skills as are laboratory techniques. There are simple rules that govern database design. The database should be simple and flexible, but provide an adequate patient profile. Entry should be standardized by precise inclusion criteria and precise definitions. Data input should be numerical whenever possible. The database program should convert simply to a comprehensive statistical program. The clinical database is useful for both observational and investigational studies. Case series, case control studies and cohort studies can all be developed from well maintained databases. In the Department of Surgery at Westmead Hospital, databases have been maintained for 10 years. The hepatobiliary and pancreatic group of databases have led to 34 publications. The liver tumour database has produced 12 studies and nearly 20 papers. The process of development of one study is outlined in detail. The chance observation of an excess incidence of gallstones in patients having regular ultrasound examinations after major abdominal surgery has been confirmed in a case control study.(ABSTRACT TRUNCATED AT 250 WORDS)

Clinical Protocols↗

PubMed2004

Cross sectional survey of multicentre clinical databases in the United Kingdom.

OBJECTIVES: To describe the multicentre clinical databases that exist in the United Kingdom, to report on their quality, to explore which organisational and managerial features are associated with high quality, and to make recommendations for improvements. DESIGN: Cross sectional survey, with interviews with database custodians and search of electronic bibliographic database (PubMed). STUDIES REVIEWED: 105 clinical databases across the United Kingdom. RESULTS: Clinical databases existed in all areas of health care, but their distribution was uneven-cancer and surgery were better covered than mental health and obstetrics. They varied greatly in age, size, growth rate, and geographical areas covered. Their scope (and thus their potential uses) and the quality of the data collected also varied. The latter was not associated with any organisational characteristics. Despite impressive achievements, many faced substantial financial uncertainty. Considerable scope existed for improvements: greater use of nationally approved codes; more support from relevant professional organisations; greater involvement by nurses, allied health professionals, managers, and laypeople in database management teams; and more attention to data security and ensuring patient confidentiality. With some notable exceptions, the audit and research potential of most databases had not been realised: half the databases had each produced only four or fewer peer reviewed research articles. CONCLUSIONS: At least one clinical database support unit is needed in the United Kingdom to provide assistance in organisation and management, information technology, epidemiology, and statistics. Without such an initiative, the variable picture of databases reported here is likely to persist and their potential not be realised.

Clinical Medicine↗

PubMed2003

Directory of clinical databases: improving and promoting their use.

BACKGROUND: The controversy surrounding the actual and potential use of clinical databases partly reflects the huge variation in their content and quality. In addition, use of existing clinical databases is severely limited by a lack of knowledge of their availability. OBJECTIVES: To develop and test a standardised method for assessing the quality (completeness and accuracy) of clinical databases and to establish a web based directory of databases in the UK. METHODS: An expert group was set up (1). to establish the criteria for inclusion of databases; (2). to develop a quality assessment instrument with high content validity, based on epidemiological theory; (3). to test empirically, modify, and retest the acceptability to database custodians, face validity and floor/ceiling effects; and (4). to design a website. RESULTS: Criteria for inclusion of databases were the provision of individual level data; inclusion in the database defined by a common circumstance (e.g. condition, treatment), an administrative arrangement, or an adverse outcome; and inclusion of data from more than one provider. A quality assessment instrument consisting of 10 items (four on coverage, six on reliability and validity) was developed and shown to have good face and content validity, no floor/ceiling effects, and to be acceptable to database custodians. A website (www.docdat.org) was developed. Indications over the first 18 months (number of visitors to the site) are that it is increasingly popular. By November 2002 there were around 3500 hits a month. CONCLUSIONS: A website now exists where visitors can identify clinical databases in the UK that may be suitable to meet their aims. It is planned both to develop a local version for use within a hospital and to encourage similar national systems in other countries.

Databases, Factual↗

PubMed2006

Impact of the revision of a nutrient database on the validity of a self-administered food frequency questionnaire (FFQ).

BACKGROUND: Revision of the national nutrient database in 2000 had a strong impact on the absolute level of estimated nutrient intake in dietary assessments. However, whether it influenced the ranking of individuals by estimated intake, a more important function in epidemiologic studies, has not been investigated. Here, we investigated the effect of this revision of the nutrient database on the validity of a food frequency questionnaire (FFQ) used to estimate nutrient intake in the Japan Public Health Center-based prospective Study (JPHC Study). METHODS: Subjects were a subsample of the JPHC Study who volunteered to participate in the validation study of the FFQ. Validity of the FFQ was evaluated by reference to the 28-day weighed dietary records as a gold standard. Nutrient intake according to the FFQ was recalculated using the revised database, and the results were compared to those using the previous database. Spearman's rank correlation coefficients (CCs) between intakes estimated by the FFQ and dietary records were computed using the revised database, and were compared to CCs computed using the previous database. RESULTS: For most of the nutrients, mean intake increased or decreased significantly using the revised database. However, no notable change was seen for the CC between estimated intake according to dietary records and FFQ when the revised database was used for calculation. Differences in the point estimates of the CCs ranged from -0.14 to 0.15. Likewise, CCs between biomarkers and estimated intake according to FFQ were similar for the two databases. CONCLUSION: Despite changes in intake levels for many nutrients, the validity of our FFQ using rank correlation by nutrient intake was not influenced by revision of the nutrient database in Japan.

Aged↗

PubMed1992

Database use in neonatal intensive care units: success or failure.

The purpose of this national survey was to define the extent and features of database use by 445 tertiary level neonatal intensive care nurseries in the United States. Of the 305 centers responding to our survey, 78% had a database in use in 1989 and 15% planned to develop one in the future. Nurseries varied remarkably in the volume of data collected, the amount of time devoted to completing data collection forms, and the personnel involved in data collection. Although data were used primarily for statistical reports (93% of nurseries), quality assurance (73%) and research activities (61%) were also enhanced by database information. Neonatal databases were used to generate reports for the permanent medical record in 38% of centers. Satisfaction with the database was dependent on how useful the database information was to centers which collected and actually used a large volume of information. Overall, nurseries expressed a high degree of confidence in the data they collected, and 65% felt their neonatal database information could be used directly in publication of research. It was disturbing that accuracy of data was not monitored formally by the majority of nurseries. Only 27% of centers followed a routine schedule of data quality assurance, and only 53% had built in error messages for data entry. We caution all who receive database information in the form of morbidity and mortality statistics, clinical reports on patients cared for in neonatal units, and published manuscripts to be attentive to the quality of the data they consume. We feel that future database design efforts need to better address data quality control. Our findings stress the importance and need for immediate efforts to better address database quality control.

Data Collection↗

PubMed1991

A protein secondary structure database (PSS).

A protein secondary structure database (PSS) has been designed to correlate the Protein Sequence Database of the PIR-International with the atomic coordinates and bond connectivities database of the Protein Data Bank in the Brookhaven National Laboratory. The present database includes secondary structures determined by X-ray diffraction analysis, but not predicted structures. The database currently contains data from both the Protein Sequence Database and the Protein Data Bank Database, and will encompass the NMR database in the future. The main characteristics of the database are as follows: (1) the secondary structures, sites, regions and domains of structural interest are displayed together with protein primary structures; and (2) the secondary structure of a desired length of peptide fragment is displayed upon request, as are the peptide fragment(s) that correspond to a defined secondary structure. This database also has software to indicate amino acid pairs having hydrogen bonds and to count the occurrence frequency of each pair as well as the conformational parameters widely used in semi-empirical methods of secondary structure prediction.

Amino Acid Sequence↗

PubMed2001

The development and implementation of a computerized database for clinical research in minimal access surgery. An international pilot study.

BACKGROUND: The measurement of outcomes after minimal access surgery (MAS) relies on the maintenance of an accurate, prospective clinical database. The development of a system for data management often proves to be challenging, expensive, and extremely time-consuming. METHODS: We developed a computerized relational database for MAS using Microsoft Access 97 to reside on a hospital server, taking advantage of existing network connections, security, and backup systems. The design of the database includes a point-and-click approach with dropdown boxes for diagnoses, procedures, and complications (limited free-text entry). A fundamental feature of this database allows surgeons and surgical trainees to record clinical information at the point and time of data acquisition. RESULTS: A "beta version" or fully functional draft of the database was presented to a group of surgeons from a variety of specialties (n = 8), and a structured interview based on a questionnaire was used to elicit the surgeon's evaluations of the database. Using the information from the interviews, the database was extensively revised and restructured. CONCLUSIONS: We have developed a relational database that reflects the needs of surgeons interested in clinical research. This database may serve as a template for other centers. It can be expanded to adopt new procedures or modified for other surgical specialties.

Attitude of Health Personnel↗

PubMed2004

Methods for automated concept mapping between medical databases.

The retrieval and exchange of information between medical databases is often impeded by the semantic heterogeneity of concepts contained within the databases. Manual identification of equivalent database elements consumes time and resources, and may often be the rate-limiting technological step in integrating disparate data sources. By employing semantic networks as an intermediary representation of the native databases, automated mapping algorithms can identify equivalent concepts in disparate databases. The algorithms take advantage of the conceptual "context" embodied within a semantic network to produce candidate concept mappings. The performance of automated concept mapping was evaluated by creating semantic network representations for two test laboratory databases. The mapping algorithms identified all equivalent concepts that were present in the databases, and did not leave any equivalent concepts unmapped. The utilization of conceptual context to perform automated concept mapping facilitates the identification of equivalent database concepts and may help decrease the work and costs associated with retrieval and integration of information from disparate databases.

Algorithms↗

PubMed1998

A model system for studying the integration of molecular biology databases.

MOTIVATION: Integration of molecular biology databases remains limited in practice despite its practical importance and considerable research effort. The complexity of the problem is such that an experimental approach is mandatory, yet this very complexity makes it hard to design definitive experiments. This dilemma is common in science, and one tried-and-true strategy is to work with model systems. We propose a model system for this problem, namely a database of genes integrating diverse data across organisms, and describe an experiment using this model. RESULTS: We attempted to construct a database of human and mouse genes integrating data from GenBank and the human and mouse genome-databases. We discovered numerous errors in these well-respected databases: approximately 15% of genes are apparently missing from the genome-databases; links between the sequence and genome-databases are missing for another 5-10% of the cases; about a third of likely homology links are missing between the genome-databases; 10-20% of entries classified as 'genes' are apparently misclassified. By using a model system, we were able to study the problems caused by anomalous data without having to face all the hard problems of database integration. CONTACT: nat@jax.org

Animals↗

PubMed1992

A profile for molecular biology databases and information resources.

This paper examines the requirements for building database management systems and multi-database information resources to support molecular biology research. The paper profiles the most important features of 16 integrated resources and 102 databases related to molecular biology research. The aspects surveyed in this paper include the nature of information in these databases, their sizes, update properties, cross-references, database management system heterogeneity, geographical distribution, data quality, use of temporal information and level of interpretation. The paper also comments on the access patterns to these databases. Since not all these aspects were available for all databases, specific comparisons sometimes compare fewer than the full 102 databases. Consequently, the same set of databases is not necessarily always being compared with respect to every aspect. The paper is organized primarily according to these comparison aspects and ends with some concluding remarks.

Databases, Bibliographic↗

PubMed2002

MIPS: a database for genomes and protein sequences.

The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences, and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the databases for the comprehensive set of genomes (PEDANT genomes), the database of annotated human EST clusters (HIB), the database of complete cDNAs from the DHGP (German Human Genome Project), as well as the project specific databases for the GABI (Genome Analysis in Plants) and HNB (Helmholtz-Netzwerk Bioinformatik) networks. The Arabidospsis thaliana database (MATDB), the database of mitochondrial proteins (MITOP) and our contribution to the PIR International Protein Sequence Database have been described elsewhere [Schoof et al. (2002) Nucleic Acids Res., 30, 91-93; Scharfe et al. (2000) Nucleic Acids Res., 28, 155-158; Barker et al. (2001) Nucleic Acids Res., 29, 29-32]. All databases described, the protein analysis tools provided and the detailed descriptions of our projects can be accessed through the MIPS World Wide Web server (http://mips.gsf.de).

Amino Acid Sequence↗

PubMed2002

The KEGG databases at GenomeNet.

The Kyoto Encyclopedia of Genes and Genomes (KEGG) is the primary database resource of the Japanese GenomeNet service (http://www.genome.ad.jp/) for understanding higher order functional meanings and utilities of the cell or the organism from its genome information. KEGG consists of the PATHWAY database for the computerized knowledge on molecular interaction networks such as pathways and complexes, the GENES database for the information about genes and proteins generated by genome sequencing projects, and the LIGAND database for the information about chemical compounds and chemical reactions that are relevant to cellular processes. In addition to these three main databases, limited amounts of experimental data for microarray gene expression profiles and yeast two-hybrid systems are stored in the EXPRESSION and BRITE databases, respectively. Furthermore, a new database, named SSDB, is available for exploring the universe of all protein coding genes in the complete genomes and for identifying functional links and ortholog groups. The data objects in the KEGG databases are all represented as graphs and various computational methods are developed to detect graph features that can be related to biological functions. For example, the correlated clusters are graph similarities which can be used to predict a set of genes coding for a pathway or a complex, as summarized in the ortholog group tables, and the cliques in the SSDB graph are used to annotate genes. The KEGG databases are updated daily and made freely available (http://www.genome.ad.jp/kegg/).

Animals↗

PubMed2006

AgdbNet - antigen sequence database software for bacterial typing.

BACKGROUND: Bacterial typing schemes based on the sequences of genes encoding surface antigens require databases that provide a uniform, curated, and widely accepted nomenclature of the variants identified. Due to the differences in typing schemes, imposed by the diversity of genes targeted, creating these databases has typically required the writing of one-off code to link the database to a web interface. Here we describe agdbNet, widely applicable web database software that facilitates simultaneous BLAST querying of multiple loci using either nucleotide or peptide sequences. RESULTS: Databases are described by XML files that are parsed by a Perl CGI script. Each database can have any number of loci, which may be defined by nucleotide and/or peptide sequences. The software is currently in use on at least five public databases for the typing of Neisseria meningitidis, Campylobacter jejuni and Streptococcus equi and can be set up to query internal isolate tables or suitably-configured external isolate databases, such as those used for multilocus sequence typing. The style of the resulting website can be fully configured by modifying stylesheets and through the use of customised header and footer files that surround the output of the script. CONCLUSION: The software provides a rapid means of setting up customised Internet antigen sequence databases. The flexible configuration options enable typing schemes with differing requirements to be accommodated.

Algorithms↗

PubMed2002

Content based information retrieval in forensic image databases.

This paper gives an overview of the various available image databases and ways of searching these databases on image contents. The developments in research groups of searching in image databases is evaluated and compared with the forensic databases that exist. Forensic image databases of fingerprints, faces, shoeprints, handwriting, cartridge cases, drugs tablets, and tool marks are described. The developments in these fields appear to be valuable for forensic databases, especially that of the framework in MPEG-7, where the searching in image databases is standardized. In the future, the combination of the databases (also DNA-databases) and possibilities to combine these can result in stronger forensic evidence.

Computer Graphics↗