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At least 1,135 records · Page 63Linked to original sources
PubMed1992

LIPIDAT: a database of lipid phase transition temperatures and enthalpy changes. DMPC data subset analysis.

The systematic study of the mesomorphic phase properties of synthetic and biologically derived lipids began some 30 years ago. In the past decade, interest in this area has grown enormously. As a result, there exists a wealth of information on lipid phase behavior, but unfortunately these data have until now been scattered throughout the literature in a variety of books, proceedings and journals. The data have recently been compiled in a centralized database, LIPIDAT, with a view to providing ready access to the data and to the appropriate literature. LIPIDAT consists of a tabulation of all known mesomorphic and polymorphic phase transition temperatures and enthalpy changes for synthetic and biologically-derived lipids in the dry and in the partially and fully hydrated states. Also included is the effect of pH, and of salt and metal ion concentration and other additives such as proteins, drugs, etc., on the thermodynamic values. The methods used in making the measurements and the experimental conditions are reported. Bibliographic information includes comprehensive literature referencing and list of authors, but does not at the present time include article titles. As of this writing, the database is current through June, 1990 and is approaching 10,000 records in length. Each record contains 28 fields. In this paper we report the contents and present an analysis of LIPIDAT as it refers to fully hydrated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). This database subset represents about 7% of all LIPIDAT records. It includes data collected over a 23-year period from 1967 to 1989 and consists of 702 records obtained from 336 articles in 55 different journals. The number of records per year rises steadily beginning in 1971, reaches a maximum of 89 records/year in 1977 and remains relatively constant at 60-70 records/year in the succeeding period. Journals making the greatest contribution to the DMPC subset include Biochimica et Biophysica Acta, Biochemistry, Chemistry and Physics of Lipids and the Biophysical Journal. These four journals account for 71% of the total records in the database subset. The analysis shows that differential scanning calorimetry, electron spin resonance, fluorescence, nuclear magnetic resonance and Raman spectroscopy are the methods most commonly used for DMPC transition temperature determination. An interesting pattern emerges as to the place in time the different methods assume or loose popularity.(ABSTRACT TRUNCATED AT 400 WORDS)

Calorimetry, Differential Scanning↗
PubMedDate not supplied

Molecular biological databases--present and future.

The importance of databases as a research tool in molecular biology is growing steadily, and a wide range of databases relevant to genome research is currently available. However, the design of current databases is inadequate for accurate representation and analysis of the results of large-scale genome mapping and sequencing projects. A new generation of databases is required to master the challenges of the future.

Animals↗
PubMed2006

Bioinformatics database infrastructure for biotechnology research.

Many databases are available that provide valuable data resources for the biotechnological researcher. According to their core data, they can be divided into different types. Some databases provide primary data, like all published nucleotide sequences, others deal with protein sequences. In addition to these two basic types of databases, a huge number of more specialized resources are available, like databases about protein structures, protein identification, special features of genes and/or proteins, or certain organisms. Furthermore, some resources offer integrated views on different types of data, allowing the user to do easy customized queries over large datasets and to compare different types of data.

Animals↗
PubMedDate not supplied

A database for tracking toxicogenomic samples and procedures.

Reproductive toxicogenomic studies generate large amounts of toxicological and genomic data. On the toxicology side, a substantial quantity of data accumulates from conventional endpoints such as histology, reproductive physiology and biochemistry. The largest source of genomics data is DNA microarrays, which generate enormous amounts of information in the course of profiling gene expression. Thus, data storage and management become essential and require a more sophisticated system than lab notebooks and electronic spreadsheets. We developed a database for tracking toxicogenomic samples and procedures (TSP 1.0) for our reproductive studies based on the MIAME-Tox guidelines and relational database theory. This database stores the various types of data from both toxicological and genomic assays in a hierarchical fashion. The user-friendly interface provides easy procedures for researchers to add, edit, save, delete, and navigate different records. Finally, TSP facilitates exporting microarray data into public databases.

Database Management Systems↗
PubMed2002

A decade of change--risk profiles and outcomes for isolated coronary artery bypass grafting procedures, 1990-1999: a report from the STS National Database Committee and the Duke Clinical Research Institute. Society of Thoracic Surgeons.

BACKGROUND: The Society of Thoracic Surgeons National Adult Cardiac Database is the largest voluntary clinical database in medicine. Using this database we examined changes in the risk profile of patients undergoing isolated coronary artery bypass grafting (CABG) and their outcomes during the decade 1990 to 1999. METHODS: Trends in 23 preoperative risk factors were tracked for CABG cases during this decade. Using a multivariate logistic risk model, we also determined the degree to which operative risk and risk-adjusted operative mortality changed during this 10-year interval. RESULTS: Between 1990 and 1999, 1,154,486 patient records were harvested by the Society of Thoracic Surgeons National Adult Cardiac Database for isolated CABG procedures performed at 522 Society of Thoracic Surgeons participant sites in the United States and Canada. Over time, CABG patients were more likely to be older (mean age 63.7 in 1990, 65.1 in 1999), of female gender (25.7% women in 1990, 28.7% in 1999), and have a history of smoking, diabetes mellitus, renal failure, hypertension, stroke, chronic lung disease, New York Heart Association functional class IV, and three-vessel disease (p < 0.0001). Patients' predicted operative risk increased by 30.1%, from 2.6% in 1990 to 3.4% in 1999. Despite higher risk, observed operative mortality decreased by 23.1%, from 3.9% in 1990 to 3.0% in 1999 (p < 0.0001). During the decade, a Medicare-aged subset (n = 629,174) experienced similar increases in risk and declines in mortality. CONCLUSIONS: Patients referred for isolated CABG are significantly older, sicker, and have a higher risk than a decade ago. Despite this, CABG mortality rates have declined substantially. These results highlight the excellent progress in the care of CABG patients achieved during the past decade.

Adult↗
PubMed1998

Updates to the Data Quality Review Program: the Society of Thoracic Surgeons Adult Cardiac National Database.

To ensure the credibility of this voluntary database, The Society of Thoracic Surgeons' National Database Audit and Validation Sub-Committee has been working during the past year to update and expand the group practice-based indicators used to assess the completeness, accuracy, and generalizability of the Adult Cardiac National Database. With increasing frequency, questions have been raised by third-party payors and regional/state-based groups as to the integrity of the data retained in the Adult Cardiac National Database. To work in conjunction with the Audit and Validation Sub-Committee to explicitly examine these issues, The Society of Thoracic Surgeons initiated a new Expert Advisory Panel review mechanism. This article describes the expanded data completeness and quality criteria that will be implemented in the coming year and summarizes the Expert Advisory Panel's recommendations for improvement.

Adult↗
PubMed2003

Constructing a database of individual clinical trials for longitudinal analysis.

Individual patient data are often required to evaluate how patient-specific factors modify treatment effects. We describe our experience combining individual patient data from 1946 subjects in 11 randomized controlled trials evaluating the effect of angiotensin-enzyme converting (ACE) inhibitors for treating nondiabetic renal disease. We sought to confirm the results of our meta-analysis of group data on the efficacy of ACE inhibitors in slowing the progression of renal disease, as well as to determine whether any study or patient characteristics modified the beneficial effects of treatment. In particular, we wanted to find out if the mechanism of action of ACE inhibitors could be explained by adjusting for follow-up blood pressure and urine protein. Each trial site sent a database of multiple files and multiple records per patient containing longitudinal data of demographic, clinical, and medication variables to the data coordinating center. The databases were constructed in several different languages using different software packages with unique file formats and variable names. Over 4 years, we converted the data into a standardized database of more than 60,000 records. We overcame a variety of problems including inconsistent protocols for measurement of key variables; varying definitions of the baseline time; varying follow-up times and intervals; differing medication-reporting protocols; missing variables; incomplete, missing, and implausible data values; and concealment of key data in text fields. We discovered that it was easier and more informative to request computerized data files and merge them ourselves than to ask the investigators to abstract partial data from their files. Although combining longitudinal data from different trials based on different protocols in different languages is complex, costly, and time-intensive, analyses based on individual patient data are extremely informative. Funding agencies must be encouraged to provide support to collaborative groups combining databases.

Angiotensin-Converting Enzyme Inhibitors↗
PubMed2002

Congenital Heart Surgery Nomenclature and Database Project: update and proposed data harvest.

In 1998, the first report of the Society of Thoracic Surgery (STS) National Congenital Heart Surgery Database reported the clinical features of 18 congenital heart categories. The report provided a significant amount of important information and also highlighted the strengths and weaknesses of the existing database. Following this report, the STS Congenital Heart Surgery Committee, in cooperation with the European Association of Cardio-Thoracic Surgery and the European Congenital Heart Surgeons Foundation, initiated the International Congenital Heart Surgery and Nomenclature Database Project. The goal was to begin the standardization of nomenclature and reporting strategies and establish the foundations for an international congenital heart surgery database. The first report of the International Congenital Heart Surgery Nomenclature Project was published in the Annals of Thoracic Surgery in April 2000. The current report outlines modifications to the minimal dataset, as well as the diagnosis and procedure short lists.

Cardiac Surgical Procedures↗
PubMed1997

An intranet database for pacemaker patients.

A database system, incorporating smartcard technologies, was designed to hold the personal and pacing details of pacemaker patients, who attended a clinic at the Royal Sussex County Hospital (RSCH), Brighton, UK. Following an initial period of a 12 month clinical trial, with the database running on a standalone personal computer, the Pacemaker Patient Database has been redesigned and implemented as an intranet-based system. This paper describes the issues relating to the development of the new prototype system and identifies the design principles for intranet-based electronic health care (EHCR) record database systems.

Computer Communication Networks↗
PubMed2026

ProteoParc: A Reference Protein Database Builder for Ancient and Nonmodel Organisms.

Over the past few years, the increasing interest in analyzing the proteome of extinct and nonmodel organisms has generated a new field of research expanding the scope of proteomics. The lack of curated databases and/or molecular data from these organisms forces researchers to manually search in different public repositories for related protein sequences, either for MS/MS peptide identification or ZooMS marker annotation. This can lead to format incongruences and hinder reproducibility between studies. To address this issue, we introduce ProteoParc, a user-friendly software that builds reference databases by systematically downloading and processing protein sequences from the most widely used public repositories. The pipeline's output is a nonredundant protein database, formatted in a way to be interpreted by typical peptide identification software. Moreover, the user can adjust the database dimension and composition by applying different criteria to include only a certain number of genes or species. Thus, ProteoParc is an easy and fast, custom-made bioinformatic tool useful for future paleoproteomics analysis in ancient samples related to understudied organisms.

Databases, Protein↗
PubMedDate not supplied

UTAB: a computer database on residues of xenobiotic organic chemicals and heavy metals in plants.

The UTAB Database contains information concerned with the uptake/accumulation, translocation, adhesion, and biotransformation of both xenobiotic organic chemicals and heavy metals by vascular plants. UTAB can be used to estimate the accumulation of chemicals in vegetation and their subsequent movement through the food chain. The database contains actual data from papers in the published literature dating from 1926 for organic chemicals and from 1976 for heavy metals. At present the database is comprised of more than 37,000 records pertaining to 900 different organic chemicals, 21 heavy metals, and over 350 plant species. Each record contains information on a single combination of species, chemical, and dose. Other information includes the application and destination sites, amount accumulated, rates of uptake or translocation, products and sites of biotransformation, experimental condition parameters, and the source paper. Thus, the database can be used to quickly obtain specific data pertaining to a chemical, plant species, mine spoil, etc. or it can be used for the comparative analysis of a set of data pertaining to groups of chemicals and plants.

Databases, Bibliographic↗
PubMed2006

Locus-specific mutation databases: pitfalls and good practice based on the p53 experience.

Between 50,000 and 60,000 mutations have been described in various genes that are associated with a wide variety of diseases. Reporting, storing and analysing these data is an important challenge as such data provide invaluable information for both clinical medicine and basic science. Locus-specific databases have been developed to exploit this huge volume of data. The p53 mutation database is a paradigm, as it constitutes the largest collection of somatic mutations (22,000). However, there are several biases in this database that can lead to serious erroneous interpretations. We describe several rules for mutation database management that could benefit the entire scientific community.

Database Management Systems↗
PubMed2002

TestisBank: an internet-based gene sequence database of the testis.

The testis is a highly transcriptionally active organ with hundreds of genes expressed during different stages of spermatogenesis. Scientists working on the testis are restricted to using two sources for further information on testicular genes, GenBank and MEDLINE. However, these two databases are not completely linked and give only very little information on the cellular type of expression or whether a gene is cloned in other tissues but is also expressed in the testis. We have generated an organ-specific database named TestisBank, which is capable of retrieving a more complete set of genes expressed in the different cell types of the testis. Furthermore, it extends to the epididymis which plays an important role in germ cell maturation. TestisBank is automatically updated to match the current status of sequence entries in the genome databases and it provides the user with an interface convenient to handle and provides useful links related to male reproduction. The TestisBank is publicly available at http://medweb.uni-muenster.de/TestisBank/. The design of the TestisBank may provide a simple model for the development of databases in which molecular and literature data are merged, thereby allowing detailed insight into the contribution of different cells/genes to the complex process of spermatogenesis.

Databases, Bibliographic↗
PubMed2006

Challenges to be faced in the reconstruction of metabolic networks from public databases.

In the post-genomic era, the biochemical information for individual compounds, enzymes, reactions to be found within named organisms has become readily available. The well-known KEGG and BioCyc databases provide a comprehensive catalogue for this information and have thereby substantially aided the scientific community. Using these databases, the complement of enzymes present in a given organism can be determined and, in principle, used to reconstruct the metabolic network. However, such reconstructed networks contain numerous properties contradicting biological expectation. The metabolic networks for a number of organisms are reconstructed from KEGG and BioCyc databases, and features of these networks are related to properties of their originating database.

Algorithms↗
PubMed1995

Characterizing heterogeneous molecular biology database systems.

Molecular biology data are distributed among multiple databases. Although containing related data, these databases are often isolated and are characterized by various degrees of heterogeneity: they usually represent different views (schemas) of the scientific domain and are implemented using different data management systems. Currently, several systems support managing data in heterogeneous molecular biology databases. Lack of clear criteria for characterizing such systems precludes comprehensive evaluations of these systems or determining their relationships in terms of shared goals and facilities. In this paper, we propose criteria that would facilitate characterizing, evaluating, and comparing heterogeneous molecular biology database systems.

Computer Communication Networks↗
PubMed2005

Biomolecular interaction network database.

This software review looks at the utility of the Biomolecular Interaction Network Database (BIND) as a web database. BIND offers methods common to related biology databases and specialisations for its protein interaction data. Searching and browsing this database is easy and well integrated with the underlying data and the needs of scientists. Interaction networks are visualised with software that offers many useful options. The innovative ontoglyphs are used throughout to provide visual cues to protein functions, localisation and other aspects one needs to know for this data set. One can expect to get useful results that may be well integrated with one's research needs.

Binding Sites↗
PubMedDate not supplied

Development of the receptor database (RDB): application to the endocrine disruptor problem.

MOTIVATION: To represent various aspects of receptors effectively, we developed the receptor database (RDB), using an object-oriented database management system ACEDB and the Internet/WWW technology. RESULTS: RDB was constructed so that the system collects data items such as attributes of proteins from distributed data sources of the Internet, and so that it provides various viewing tools effectively, depending on different types of receptor data. Such sources include standard international biological databases such as the up-to-date database of PIR, Swiss Prot, PDB, GenBank and GDB. Application to the endocrine disruptor problem is presented. AVAILABILITY: RDB is available through the Internet at http://impact.nihs.go.jp/RDB.html.

Amino Acid Sequence↗
PubMed2002

Tolerating some redundancy significantly speeds up clustering of large protein databases.

MOTIVATION: Sequence clustering replaces groups of similar sequences in a database with single representatives. Clustering large protein databases like the NCBI Non-Redundant database (NR) using even the best currently available clustering algorithms is very time-consuming and only practical at relatively high sequence identity thresholds. Our previous program, CD-HI, clustered NR at 90% identity in approximately 1 h and at 75% identity in approximately 1 day on a 1 GHz Linux PC (Li et al., Bioinformatics, 17, 282, 2001); however even faster clustering speed is needed because the size of protein databases are rapidly growing and many applications desire a lower attainable thresholds. RESULTS: For our previous algorithm (CD-HI), we have employed short-word filters to speed up the clustering. In this paper, we show that tolerating some redundancy makes for more efficient use of these short-word filters and increases the program's speed 100 times. Our new program implements this technique and clusters NR at 70% identity within 2 h, and at 50% identity in approximately 5 days. Although some redundancy is present after clustering, our new program's results only differ from our previous program's by less than 0.4%.

Algorithms↗