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PubMed2005

Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.

A contig-oriented database for annotation of the rice genome has been constructed to facilitate map-based rice genomics. The Rice Annotation Database has the following functional features: (i) extensive effort of manual annotations of P1-derived artificial chromosome/bacterial artificial chromosome clones can be merged at chromosome and contig-level; (ii) concise visualization of the annotation information such as the predicted genes, results of various prediction programs (RiceHMM, Genscan, Genscan+, Fgenesh, GeneMark, etc.), homology to expressed sequence tag, full-length cDNA and protein; (iii) user-friendly clone / gene query system; (iv) download functions for nucleotide, amino acid and coding sequences; (v) analysis of various features of the genome (GC-content, average value, etc.); and (vi) genome-wide homology search (BLAST) of contig- and chromosome-level genome sequence to allow comparative analysis with the genome sequence of other organisms. As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results including 30 000 manually curated genes. The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome. The database can be accessed at http://rad.dna.affrc.go.jp/.

Chromosomes, Plant↗

PubMed2003

RettBASE: The IRSA MECP2 variation database-a new mutation database in evolution.

Rett syndrome (RTT) is a neurodevelopmental disorder affecting primarily females, with an incidence of around 1 in 15,000 females. In 1999, mutations in the X-linked gene methyl-CpG-binding protein 2 (MECP2) were first reported in RTT subjects, and since that time there have been a number of publications describing cohorts of patients and their mutations. In addition, MECP2 mutations have been reported in patients who do not fit the diagnostic criteria for Rett syndrome. We have developed a new locus-specific database, RettBASE (http://mecp2.chw.edu.au/), loosely based on the PAHdb website. The aim is to obtain data relating to all known instances of MECP2 variations, including published ta and data directly submitted by one of various means (either by using an online submission form, or by sending the same form in Adobe portable document format (pdf) or Microsoft Word format by email or fax to the database curators). The database has a range of query capabilities, allowing for simple or complex interrogation of the database. To address the issue of patient confidentiality, we have incorporated an Excel spreadsheet algorithm that allows the generation of a unique number based on the subject's name and date of birth. We believe this database will prove to be a useful resource, allowing the development of accurate prevalence data for disease-causing mutations, providing a catalog of polymorphisms, and potentially allowing more accurate phenotype-genotype correlations to be drawn.

Chromosomal Proteins, Non-Histone↗

PubMed1999

Risk stratification for cardiac valve replacement. National Cardiac Surgery Database. Database Committee of The Society of Thoracic Surgeons.

BACKGROUND: The Society of Thoracic Surgeons National Database Committee is committed to risk stratification and assessment as integral elements in the practice of cardiac operations. The National Cardiac Surgery Database was created to analyze data from subscribing institutions across the country. We analyzed the database for valve replacement procedures with and without coronary artery bypass grafting to determine trends in risk stratification. METHODS: The database contains complete records of 86,580 patients who had valve replacement procedures at the participating institutions between 1986 and 1995, inclusive. The 1995 harvest of data was conducted in late 1996 and available for evaluation in 1997. These records were used to conduct an in-depth analysis of risk factors associated with valve replacement and to provide prediction of operative death by using regression analysis. Regression models were made for six subgroups. RESULTS: Adverse patient risk factors, including diabetes, hypertension and reoperation, but not ventricular function, increased over time. There were trends with regard to increasing age of the various population subsets. The types of prostheses used remained similar over time, with more mechanical prostheses than bioprostheses used for both aortic and mitral valve replacement. There was a trend toward increased use of bioprostheses in aortic replacements and decreased use in mitral replacements between 1991 and 1995 than between 1986 and 1990. The mortality rate was determined by patient subset for primary operation and reoperation and by urgency status. The modeling showed that the predicted and observed mortality correlated for all age groups and within patient subsets. CONCLUSIONS: Risk modeling is a valuable tool for predicting the probability of operative death in any individual patient. This large, multiinstitutional database is capable of determining modern operative risk and should provide standards for acceptable care. The study illustrates the importance of risk stratification for early death both for the patient and the surgeon.

Adult↗

PubMed1999

GXD: a gene expression database for the laboratory mouse. The Gene Expression Database Group.

The Gene Expression Database (GXD) is a community resource that stores and integrates expression information for the laboratory mouse, with a particular emphasis on mouse development, and makes these data freely available in formats appropriate for comprehensive analysis. GXD is implemented as a relational database and integrated with the Mouse Genome Database (MGD) to enable global analysis of genotype, expression and phenotype information. Interconnections with sequence databases and with databases from other species further extend GXD's utility for the analysis of gene expression data. GXD is available through the Mouse Genome Informatics Web Site at http://www.informatics.jax.org/

Animals↗

PubMed2001

IMGT/HLA Database--a sequence database for the human major histocompatibility complex.

The IMGT/HLA Database (www.ebi.ac.uk/imgt/hla/) specialises in sequences of polymorphic genes of the HLA system, the human major histocompatibility complex (MHC). The HLA complex is located within the 6p21.3 region on the short arm of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and these include the 21 highly polymorphic HLA genes, which influence the outcome of clinical transplantation and confer susceptibility to a wide range of non-infectious diseases. The database contains sequences for all HLA alleles officially recognised by the WHO Nomenclature Committee for Factors of the HLA System and provides users with online tools and facilities for their retrieval and analysis. These include allele reports, alignment tools and detailed descriptions of the source cells. The online IMGT/HLA submission tool allows both new and confirmatory sequences to be submitted directly to the WHO Nomenclature Committee. The latest version (release 1.7.0 July 2000) contains 1220 HLA alleles derived from over 2700 component sequences from the EMBL/GenBank/DDBJ databases. The HLA database provides a model which will be extended to provide specialist databases for polymorphic MHC genes of other species.

Alleles↗

PubMed2003

The Pediatric Economic Database Evaluation (PEDE) Project: establishing a database to study trends in pediatric economic evaluation.

BACKGROUND: While standard methods for conducting economic evaluations have evolved, little attention has been paid to the conduct of these studies in special populations such as children. OBJECTIVES: To build a database of pediatric economic evaluations and to examine trends in publication characteristics over a 20-year period. RESEARCH DESIGN: The database was created through a multisource search strategy, manual review, application of inclusion/exclusion criteria, data extraction, and reliability assessment. Descriptive statistics were used to summarize trends in publication volume, disease category, intervention type, and age group between 1980 and 1999. RESULTS: From an initial cut of 5600 citations identified from 12 journal databases, 787 were included as full pediatric economic evaluations. Volume of publications increased 7-fold between 1980 to 1984 and 1995 to 1999 from 61 to 440 citations per 5-year period. Most studies were performed in children aged 1 to 12 years, and studies in infants displayed an increasing frequency. The most common disease category was infective/parasitic, comprising 24% of studies. Studies of congenital anomalies and complications of pregnancy were also prominent. Although health prevention studies were the most prevalent, health treatment studies demonstrated an equal frequency in 1995 to 1999. Most studies consisted of malaria control and vaccination strategies for hepatitis B, Haemophilus influenzae type B, measles, and varicella. CONCLUSIONS: The number of pediatric economic evaluations is steadily increasing with most publications representing health prevention interventions. The Pediatric Economic Database Evaluation (PEDE) Project database will be valuable to health researchers working in methods research and conducting systematic reviews.

Age Distribution↗

PubMed2001

The Ligand Gated Ion Channel database: an example of a sequence database in neuroscience.

Multiple comparisons of receptor sequences, or receptor subunit sequences, has proved to be an invaluable tool in modern pharmacological investigations. Although of outstanding importance, general sequence databases suffer from several imperfections due to their size and their non-specificity. Room therefore exists for expert-maintained databases of restricted focus, where knowledge of the research field helps to filter the huge amount of data generated. Accordingly, neuroscientists have designed databases covering several types of proteins, in particular receptors for neurotransmitters. Ligand-gated ion channels are oligomeric transmembrane proteins involved in the fast response to neurotransmitters. All these receptors are formed by the assembly of homologous subunits, and an unexpected wealth of genes coding for these subunits has been revealed during the last two decades. The Ligand Gated Ion Channel database (LGICdb) has been developed to handle this growing body of information. The database aims to provide only one entry for each gene, containing annotated nucleic acid and protein sequences.

Amino Acid Sequence↗

PubMed2000

Human membrane transporter database: a Web-accessible relational database for drug transport studies and pharmacogenomics.

The human genome contains numerous genes that encode membrane transporters and related proteins. For drug discovery, development, and targeting, one needs to know which transporters play a role in drug disposition and effects. Moreover, genetic polymorphisms in human membrane transporters may contribute to interindividual differences in the response to drugs. Pharmacogenetics, and, on a genome-wide basis, pharmacogenomics, address the effect of genetic variants on an individual's response to drugs and xenobiotics. However, our knowledge of the relevant transporters is limited at present. To facilitate the study of drug transporters on a broad scale, including the use of microarray technology, we have constructed a human membrane transporter database (HMTD). Even though it is still largely incomplete, the database contains information on more than 250 human membrane transporters, such as sequence, gene family, structure, function, substrate, tissue distribution, and genetic disorders associated with transporter polymorphisms. Readers are invited to submit additional data. Implemented as a relational database, HMTD supports complex biological queries. Accessible through a Web browser user interface via Common Gateway Interface (CGI) and Java Database Connection (JDBC), HMTD also provides useful links and references, allowing interactive searching and downloading of data. Taking advantage of the features of an electronic journal, this paper serves as an interactive tutorial for using the database, which we expect to develop into a research tool.

Databases, Protein↗

PubMedDate not supplied

Development of an experimental hospital database system using a relational database management system.

The development of an integrated database system for the satisfactory support of the information processing requirements of a modern hospital is clearly a major task with many associated problems. A design and implementation procedure for the development of a relational hospital database system based on an experimental relational database management system is presented which should help overcome some of the problems currently encountered. A brief outline of the application and the underlying database management system is given and a standardized procedure for the design of the multilevel database schemata is presented. The associated problems and procedures required for such a development are also examined and a number of theoretical conclusions and claims are tested in a real life application environment.

Database Management Systems↗

PubMed2001

Agreement in race-ethnicity coding between a hospital discharge database and another database.

OBJECTIVE: This study assessed the agreement in coding of race and Hispanic ethnicity for the same patients in a hospital discharge database and another database. METHODS: Race-ethnicity coding was examined for 72,276 cancer patients discharged from Connecticut hospitals (1992-1997) who were linked with the statewide cancer registry that included information on birthplace (for 76% of patients) and surname (for all patients). Surnames in the cancer registry were also linked with a list of Spanish surnames, to improve ascertainment of ethnicity among patients of probable Hispanic origin. RESULTS: Kappa coefficients (kappa) indicated substantial agreement (beyond that expected by chance) for White (kappa = .74) and Black (kappa = .93) race, Hispanic ethnicity (kappa = .73) and non-Hispanic White race-ethnicity (kappa = .83) categories. Kappa was moderate (ie, .52) for the Asian-Pacific Islander race category. Only 42% of Asian-Pacific Islanders and 62% of Hispanics in the cancer registry were similarly coded in the discharge database. CONCLUSIONS: Although both databases are imperfect, the findings suggest that ascertainment of certain racial-ethnic groups in hospital discharge databases could be improved if birthplace and surname were available.

Connecticut↗

PubMed2002

Development of a Virtual Private Database for a multi-institutional Internet-based Radiation Oncology Database overcoming differences in protocols.

A multi-institutional Radiation Oncology Greater Area Database (ROGAD) was started in 1991 under the direction of the Japanese Society for Therapeutic Radiology and Oncology (JASTRO). Use of ROGAD was intended to allow reflection of results of data analysis into treatment strategy and treatment planning for individual cases, to provide quality assurance, to maximize the efficacy of radiotherapy, to allow assessment of new technologies or new modalities, and to optimize medical decision making. ROGAD collected 13,448 radiotherapy treatment cases from 325 facilities during the period from 1992 to 2001. In 2000, questionnaires were sent to 725 radiotherapy facilities throughout Japan, to further obtain the situation of the radiation oncology database. Workers at 179 facilities replied that"the protocol of my facility is different from ROGAD protocol and I must send data according to the ROGAD protocol". So, we developed the Virtual Private Database System (VPDS) which is operated as if an oncologist had a database solely owned by his own facility, in spite of actually operating ROGAD. VPDS realizes integration of different plural databases, regardless of differences in entry methods, protocols, definitions and interpretations of contents of clinical data elements between facilities.

Clinical Protocols↗

PubMed2006

Landscape of current toxicity databases and database standards.

Having readily available historical information for modeling toxicity has become important throughout the various stages of research and development. The high cost of late-phase attrition and recent international regulatory legislations have made even more acute the need to be able to mine the fragmented data and information available across diverse databases. In addition, the general trend to accelerate regulatory processes globally makes the effective use of existing data an imperative. To achieve efficient screening, develop profiles and gain the ability to cross reference, databases must be interoperated to allow data exchange and integration. Several database standards and controlled vocabulary initiatives have been used in the development of toxicity data models to transform the current landscape. This review describes the major databases of toxicological information now available, and provides a simple example of standardization that demonstrates the benefits of a toxicity database containing such qualified data.

Animals↗

PubMed1995

The protein disease database of human body fluids: I. Rationale for the development of this database.

We are developing a relational database to facilitate quantitative and qualitative comparisons of proteins in human body fluids in normal and disease states. For decades researchers and clinicians have been studying proteins in body fluids such as serum, plasma, cerebrospinal fluid and urine. Currently, most clinicians evaluate only a few specific proteins in a body fluid such as plasma when they suspect that a patient has a disease. Now, however, high resolution two-dimensional protein electrophoresis allows the simultaneous evaluation of 1,500 to 3,000 proteins in complex solutions, such as the body fluids. This and other high resolution methods have encouraged us to collect the clinical data for the body fluid proteins into an easily accessed database. For this reason, it has been constructed on the Internet World Wide Web (WWW) under the title Protein Disease Database (PDD). In addition, this database will provide a linkage between the disease-associated protein alterations and images of the appropriate proteins on high-resolution electrophoretic gels of the body fluids. This effort requires the normalization of data to account for variations in methods of measurement. Initial efforts in the establishment of the PDD have been concentrated on alterations in the acute-phase proteins in individuals with acute and chronic diseases. Even at this early stage in the development of our database, it has proven to be useful as we have found that there appear to be several common acute-phase protein alterations in the plasma and cerebrospinal fluid from patients with Alzheimer's disease, schizophrenia and major depression. Our goal is to provide access to the PDD so that systematic correlations and relationships between disease states can be examined and extended.

Body Fluids↗

PubMed1995

The use of prescription claims databases in pharmacoepidemiological research: the accuracy and comprehensiveness of the prescription claims database in Québec.

Despite the potential benefits of using prescription claims databases for pharmacoepidemiological research, little work has been reported on the nature of available information or its accuracy. The purpose of this study was to describe information contained within the prescription claims database in Québec, and to assess the accuracy of drug information that might be used to monitor drug exposure and physician prescribing. The comprehensiveness of the prescriptions claims database was assessed by examining 1,917,214 records of dispensed prescriptions for a regionally stratified random sample of 65,349 Québec elderly in 1990. We found that values in key fields (individual identifiers, drug, quantity, date dispensed and duration) were missing or out of range in 0-0.4% of records. The accuracy of data were examined in 723 prescriptions filled by 306 elderly patients attending one internal medicine clinic. Of these prescriptions, 83% were filled by the patient and correctly identified the patient and drug and in 89% of these 599 records, the prescribing physician was correctly identified. The quantity and duration of the prescriptions were accurate in 69.1% and 72.1% of records, respectively. We conclude that the prescription claims database in Québec may represent one of the most accurate means of determining drugs dispensed to individuals. There may be limitations in using this database for dosing information.

Drug Prescriptions↗

PubMed2005

A novel approach for incremental uncertainty rule generation from databases with missing values handling: application to dynamic medical databases.

Current approaches for mining association rules usually assume that the mining is performed in a static database, where the problem of missing attribute values does not practically exist. However, these assumptions are not preserved in some medical databases, like in a home care system. In this paper, a novel uncertainty rule algorithm is illustrated, namely URG-2 (Uncertainty Rule Generator), which addresses the problem of mining dynamic databases containing missing values. This algorithm requires only one pass from the initial dataset in order to generate the item set, while new metrics corresponding to the notion of Support and Confidence are used. URG-2 was evaluated over two medical databases, introducing randomly multiple missing values for each record's attribute (rate: 5-20% by 5% increments) in the initial dataset. Compared with the classical approach (records with missing values are ignored), the proposed algorithm was more robust in mining rules from datasets containing missing values. In all cases, the difference in preserving the initial rules ranged between 30% and 60% in favour of URG-2. Moreover, due to its incremental nature, URG-2 saved over 90% of the time required for thorough re-mining. Thus, the proposed algorithm can offer a preferable solution for mining in dynamic relational databases.

Algorithms↗

PubMed1989

The REF52 protein database. Methods of database construction and analysis using the QUEST system and characterizations of protein patterns from proliferating and quiescent REF52 cells.

The construction and analysis of protein databases using the QUEST system is described, and the REF52 protein database is presented. A protein database provides the means to store and compare quantitative and descriptive data for up to 2000 proteins from many experiments that employ computer-analyzed two-dimensional gel electrophoresis. The QUEST system provides the tools to manage, analyze, and communicate these data. The REF52 database contains experiments with normal and transformed rat cell lines. In this report, many of the proteins on the REF52 map are identified by name, by subcellular localization, and by mode of post-translational modification. The quantitative experiments analyzed and compared here include 1) a study of the quantitative reproducibility of the analysis system, 2) a study of the clonal reproducibility of REF52 cells, 3) a study of growth-related changes in REF52 cells, and 4) a study of the effects of labeling cells for varying lengths of time. Of the proteins analyzed from REF52 cells, 10% are nuclear, 6% are phosphoproteins, and 4% are mannose-labeled glycoproteins. The mannose-labeled proteins are more prominent in patterns from quiescent cells, while the synthesis of cytoskeletal proteins is generally repressed at quiescence. A small set of proteins, selected for elevated rates of synthesis is generally repressed at quiescence. A small set of proteins, selected for elevated rates of synthesis in quiescent versus proliferating cells includes one of the tropomyosin isoforms, a myosin light chain isoform, and several prominent glycoproteins. These proteins are thought to be characteristic of the differentiated state of untransformed REF52 cells. Proteins induced early versus late after refeeding quiescent cells show very different patterns of growth regulation. These studies lay the foundations of the REF52 database and provide information needed to interpret the experiments with transformed REF52 cells, which are reported in the accompanying paper (Garrels, J., and Franza, B. R., Jr. (1989) J. Biol. Chem. 264, 5299-5312).

Animals↗

PubMed2000

UMD (Universal mutation database): a generic software to build and analyze locus-specific databases.

The human genome is thought to contain about 80,000 genes and presently only 3,000 are known to be implicated in genetic diseases. In the near future, the entire sequence of the human genome will be available and the development of new methods for point mutation detection will lead to a huge increase in the identification of genes and their mutations associated with genetic diseases as well as cancers, which is growing in frequency in industrial states. The collection of these mutations will be critical for researchers and clinicians to establish genotype/phenotype correlations. Other fields such as molecular epidemiology will also be developed using these new data. Consequently, the future lies not in simple repositories of locus-specific mutations but in dynamic databases linked to various computerized tools for their analysis and that can be directly queried on-line. To meet this goal, we devised a generic software called UMD (Universal Mutation Database). It was developed as a generic software to create locus-specific databases (LSDBs) with the 4(th) Dimension(R) package from ACI. This software includes an optimized structure to assist and secure data entry and to allow the input of various clinical data. Thanks to the flexible structure of the UMD software, it has been successfully adapted to nine genes either involved in cancer (APC, P53, RB1, MEN1, SUR1, VHL, and WT1) or in genetic diseases (FBN1 and LDLR). Four new LSDBs are under construction (VLCAD, MCAD, KIR6, and COL4A5). Finally, the data can be transferred to core databases.

Chromosome Mapping↗

PubMed2003

The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD).

BACKGROUND: The power of microarray analysis can be realized only if data is systematically archived and linked to biological annotations as well as analysis algorithms. DESCRIPTION: The Longhorn Array Database (LAD) is a MIAME compliant microarray database that operates on PostgreSQL and Linux. It is a fully open source version of the Stanford Microarray Database (SMD), one of the largest microarray databases. LAD is available at http://www.longhornarraydatabase.org CONCLUSIONS: Our development of LAD provides a simple, free, open, reliable and proven solution for storage and analysis of two-color microarray data.

Database Management Systems↗