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PubMed2002

Virtues of a worldwide congenital heart surgery database.

The rationale for a congenital heart surgery database lies in the organized manner in which information can be compiled to accomplish programmatic evaluation, monitor clinical outcomes, comply with governmental requirements, perform retrospective and prospective clinical studies, and participate in local, national, and global improvement strategies. The task of inaugurating an effective congenital heart surgery database has taken many years and involved concurrent development efforts at multiple sites. Two such efforts took place in North America with the Society of Thoracic Surgeons Congenital Heart Surgery Database, and in Europe with the European Congenital Heart Defects Database. These initial efforts provided the impetus for development of an international congenital heart surgery database that would allow scientific exchanges on an international scale and promote multi-institutional evaluation of congenital heart surgery. Sample outcome templates from the Society of Thoracic Surgeons and the European Association for Cardio-thoracic Surgery's accepted minimum database data set are reviewed for the specific diagnostic entry ventricular septal defect, to familiarize the reader with potential available data summaries and outcome analyses, including risk stratification, when data harvest is performed. In Europe, the agreed upon minimum data set are now collected as part of the Pediatric European Cardiac Surgical Registry, while in North America users of the CardioAccess database and users of the minimum data set downloaded from the Society of Thoracic Surgeons web site are being notified of plans for a 2002 data harvest incorporating the minimum database data set. It is likely that the extant voluntary, minimal data set congenital heart surgery database will be replaced by a mandated system required by states, provinces, and countries. Data collection schemes and data validation programs will become standardized, which will result in improved data quality and uniform congenital heart center participation. As participation with valid data approaches 100% of congenital heart centers, the power and importance of the database increases exponentially. Reliable information can be used to assess residency/fellowship programs, resource allocation, major therapeutic trends, manpower issues, and in the end, all initiatives that will require accurate information.

Databases, Factual↗
PubMed2003

Food and dietary supplement databases for What We Eat in America-NHANES.

Relative strengths and potential approaches for improvement of food and dietary supplement databases used for tabulating intakes from the dietary component of the What We Eat in America-National Health and Nutrition Examination Survey (NHANES) are discussed. The U.S. Department of Agriculture's Nutrient Data Laboratory develops and maintains the Nutrient Databank System (NDBS) and many nutrient-specific and population-specific databases. NDBS contains data for approximately 8,000 foods and approximately 115 components; tables for compounds of special interest are also available. Nutrient databases need constant revision because of a constantly changing food supply. The completeness of analytical data varies from nutrient to nutrient. The National Center for Health Statistics developed and maintains a database of dietary supplements based on label information. To date, no verification of ingredients has been undertaken. The development of a dietary supplement database containing analytical values would require extensive resources but would be valuable. Databases for vitamin and mineral supplements are compatible with food databases. Databases for botanicals and other supplements include nonnutrient constituents that may not be documented in food composition databases. Gaps in food and dietary supplement composition data exist because of limited resources, changing availability of foods and products and the advent of new compounds of health interest. More data are needed on nutrients and other bioactive constituents in foods and dietary supplements. Analytical methods do not exist for all ingredients or active constituents in foods and dietary supplements. Research needs for further development of meaningful food and dietary supplement databases are similar.

Databases, Factual↗
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↗
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↗
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↗
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↗
PubMed1998

Automatic query mapping among genomic databases: a pilot exploration.

As databases in the human genome project proliferate, it is important for users of one genomic database to identify similar or inconsistent data in other autonomously developed genomic databases. To do so, the user needs to issue the same query across multiple databases. We describe an approach that allows a query issued against one database to be automatically mapped to an equivalent query against another structurally different database. Our approach features two components: 1) a database designed to capture knowledge (metadata) that describes the correspondences among individual database components and 2) a module that utilizes the metadata to perform query mappings. As a demonstration, we apply our query mapping approach to two chromosome map databases (DB/12 and GDB).

Algorithms↗
PubMed1991

The rat liver epithelial (RLE) cell protein database.

Computer databases of rat liver epithelial (RLE) cellular polypeptides have been established using high resolution two-dimensional gel electrophoresis and computer-assisted analysis. Databases have been constructed utilizing both [35S]methionine- and [32P]orthophosphate-labeled as well as silver-stained polypeptides from normal RLE cells. The RLE database, which contains both qualitative and quantitative annotations, includes experiments with normal, chemically and oncogene transformed as well as spontaneously transformed cell lines. A total of 2537 [35S]methionine-labeled polypeptides from whole cell lysates (1920 acidic and 617 basic, separated in the first dimension using isoelectric focusing and nonequilibrium pH gradient electrophoresis, respectively) were analyzed and databases constructed using the Elsie 5 gel analysis system. To increase the "viewing window" and hence the usefulness of the RLE database, subcellular fractionation of whole cell preparations was performed and high resolution two-dimensional maps of the individual subcellular components were constructed. Databases representing 1229 cytosolic, 1539 acidic and 674 basic nuclear, 1746 membrane-associated, 415 mitochondrial, 773 in vitro translated and 350 phosphoproteins were established from these maps. The RLE databases contain the Elsie 5 identification number, protein name (if known), molecular weight and pI information, quantitative and spot shape data, and specific information regarding transformation-sensitive, growth-related (exponentially proliferating versus confluent) cell populations as well as those polypeptides modulated by specific growth factors. The RLE databases represent initial efforts toward the establishment of comprehensive databases of rat liver proteins and serve as a vital resource for on-going as well as future studies regarding the regulation of growth and differentiation as well as transformation of RLE cells.

Animals↗
PubMed1993

An efficient disk based data structure for rapid searching of quantitative two-dimensional gel databases.

Fast access of two-dimensional (2-D) gel quantitative databases is important for rapid searching for protein differences between sets of 2-D gels from an experiment. The GELLAB-II system organizes corresponding spots from the gels in the database into reference or "Rspot" sets. These Rspot numeric names index fixed regions in the paged composite gel database file. This is adequate for an existing database, but has several problems. (i) Building the initial database requires guessing how much disk space to pre-allocate for each corresponding spot (i.e. spots from different gels). If it ever runs out of pre-allocated space during this process, it must expand the size of each corresponding set of spots copying the old database data into the new in-place on the disk. (ii) When adding new gels or editing the database, if a new spot is created, the system may also go into this expansion mode. The time spent and wasted disk space can be appreciable--depending on the size of the database (order of 100 gel database). (iii) Because each set of corresponding spots is the same size, we waste space in most spot sets since they do not require the additional space a few spot sets require which contain additional fragmented spots. We present a new low-level disk object-based structure and algorithm, paged indexed buckets (PIB), which optimizes disk space usage while having similar retrieval speed to the original method.

Algorithms↗