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PubMed1998

HOMSTRAD: a database of protein structure alignments for homologous families.

We describe a database of protein structure alignments for homologous families. The database HOMSTRAD presently contains 130 protein families and 590 aligned structures, which have been selected on the basis of quality of the X-ray analysis and accuracy of the structure. For each family, the database provides a structure-based alignment derived using COMPARER and annotated with JOY in a special format that represents the local structural environment of each amino acid residue. HOMSTRAD also provides a set of superposed atomic coordinates obtained using MNYFIT, which can be viewed with a graphical user interface or used for comparative modeling studies. The database is freely available on the World Wide Web at: http://www-cryst.bioc.cam. ac.uk/-homstrad/, with search facilities and links to other databases.

Aspartic Acid Endopeptidases↗
PubMed2005

RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank.

State-of-the-art methods based on CNS and CYANA were used to recalculate the nuclear magnetic resonance (NMR) solution structures of 500+ proteins for which coordinates and NMR restraints are available from the Protein Data Bank. Curated restraints were obtained from the BioMagResBank FRED database. Although the original NMR structures were determined by various methods, they all were recalculated by CNS and CYANA and refined subsequently by restrained molecular dynamics (CNS) in a hydrated environment. We present an extensive analysis of the results, in terms of various quality indicators generated by PROCHECK and WHAT_CHECK. On average, the quality indicators for packing and Ramachandran appearance moved one standard deviation closer to the mean of the reference database. The structural quality of the recalculated structures is discussed in relation to various parameters, including number of restraints per residue, NOE completeness and positional root mean square deviation (RMSD). Correlations between pairs of these quality indicators were generally low; for example, there is a weak correlation between the number of restraints per residue and the Ramachandran appearance according to WHAT_CHECK (r = 0.31). The set of recalculated coordinates constitutes a unified database of protein structures in which potential user- and software-dependent biases have been kept as small as possible. The database can be used by the structural biology community for further development of calculation protocols, validation tools, structure-based statistical approaches and modeling. The RECOORD database of recalculated structures is publicly available from http://www.ebi.ac.uk/msd/recoord.

Databases, Protein↗
PubMedDate not supplied

The peptaibol database: a sequence and structure resource.

The peptaibols are a large family of membrane-active peptides with considerable sequence homology, but with different biological properties and three-dimensional structures. They constitute a rich resource of naturally occurring 'mutants' which are potentially valuable for structure/function studies of ion channels. A searchable on-line database of sequences and structures of the peptaibols has been created at http://www.cryst.bbk.ac.uk/peptaibol, as a resource for the biological and structural community. In this paper, the contents and organization of the website are discussed as well as procedures for submission of new entries to the database. At present, more than 300 peptaibol sequences are stored in the database. Each sequence entry contains its full literature reference and information about its biological source. Tools are provided for searching for specific peptaibol sequences or groupings of sequences, and for locating peptaibols containing specified sequence motifs. In addition the website acts as a database for structural information. The coordinates of all currently available peptaibol x-ray and NMR structures are included and complemented, where appropriate. with molecular graphics illustrations. These include figures of model channel structures and comparisons between different peptaibol structures. The peptaibol database thus provides a tool for ready access to information and a means of investigating the sequences and structures of this class of polypeptides.

Amino Acid Sequence↗
PubMed1994

Protein family classification based on searching a database of blocks.

The most highly conserved regions of proteins can be represented as "blocks" of locally aligned sequence segments. Previously, an automated system was introduced to generate a database of blocks that is searched for local similarities using a sequence query. Here, we describe a method for searching this database that can also reveal significant global similarities. Local and global alignments are scored independently, so they can be used in concert to infer homology. A set of 7082 diverse sequences not represented in the database provided queries for testing this approach. The resulting distributions of scores led to guidelines for interpretation of search data and to the classification of 289 uncatalogued sequences into known groups. Thirty-eight of these relationships appear to be new discoveries. We also show how searching a database of blocks can be used to detect repeated domains and to find distinct cross-family relationships that were missed in searches of sequence databases.

Animals↗
PubMed1996

FASTA-SWAP and FASTA-PAT: pattern database searches using combinations of aligned amino acids, and a novel scoring theory.

We introduce two new pattern database search tools that utilize statistical significance and information theory to improve protein function identification. Both the general pattern scoring theory with the specific matrices introduced here and the low redundancy of pattern databases increase search sensitivity and selectivity. Pattern scoring preferentially rewards matches at conserved positions in a pattern with higher scores than matches at variable positions, and assigns more negative scores to mismatches at conserved positions than to mismatches at variable positions. The theory of pattern scoring can be used to create log-odds pattern scores for patterns derived from any set of multiple alignments. This theoretical framework can be used to adapt existing sequence database search tools to pattern analysis. Our FASTA-SWAP and FASTA-PAT tools are extensions of the FASTA program that search a sequence query against a pattern database. In the first step, FASTA-SWAP searches the diagonals of the query sequence and the library pattern for high-scoring segments, while FASTA-PAT performs an extended version of hashing. In the second step, both methods refine the alignments and the scores using dynamic programming. The tools utilize an extremely compact binary representation of all possible combinations of amino acid residues in aligned positions. Our FASTA-SWAP and FASTA-PAT tools are well suited for functional identification of distant relatives that may be missed by sequence database search methods. FASTA-SWAP and FASTA-PAT searches can be performed using our World-Wide Web Server (http://dot.imgen.bcm.tmc.edu:9331/seq-search/Op tions/fastapat.html).

Algorithms↗
PubMed2000

PACS databases and enrichment of the folder manager concept.

Current challenges facing picture archiving and communication systems (PACS) center around database design and functionality. Workflow issues and folder manager concepts such as autorouting, prefetching, hanging protocols, and hierarchical storage management are driven by a properly designed database that ultimately directly impacts the clinical utility of a PACS. The key issues in PACS database design that enable radiologist-friendly, cost-effective, and data-secure systems will be discussed, including database difficulties of the DICOM standard, HIS/RIS/PACS (hospital information system/radiology information system) connectivity, and database issues in data acquisition, data dissemination, and data display.

Databases as Topic↗
PubMed2001

Conceptual database modeling: a method for enabling end users (radiologists) to understand and develop their information management applications.

As medical technology advances at a rapid pace, clinicians become further and further removed from the design of their own technological tools. This is particularly evident with information management. For radiologists, clinical histories, patient reports, and other pertinent information require sophisticated tools for data handling. However, as databases grow more powerful and sophisticated, systems require the expertise of programmers and information technology personnel. The radiologist, the clinician end-user, must maintain involvement in the development of system tools to insure effective information management. Conceptual database modeling is a design method that serves to bridge the gap between the technological aspects of information management and its clinical applications. Conceptual database modeling involves developing information systems in simple language so that anyone can have input into the overall design. This presentation describes conceptual database modeling, using object role modeling, as a means by which end-users (clinicians) may participate in database development.

Database Management Systems↗
PubMed2004

[Databases as a source for monitoring systems of drug safety].

Clinical trials only allow for a limited assessment of adverse drug reactions (ADRs) due to their restricted number of patients, their short duration, and their narrow inclusion criteria. To assess potential ADRs in the population actually treated after drug approval, different systems for signal generation such as spontaneous reporting systems have been established and are required by drug laws in many countries. As of today epidemiological methods for signal confirmation for rare adverse events or events with long induction periods use record linkage databases such as the United Health Care (Ingenix) in the USA or the practice databases such as the General Practice Research Database in Great Britain. However, this approach also has its limitations. This type of database will be presented in this paper. In addition, databases operated by German public health insurance will be described. The topic of linking different data sources in Germany to support pharmaco-vigilance activities will be addressed.

Adverse Drug Reaction Reporting Systems↗
PubMed2006

A referent bone mineral density database for Chinese American women.

INTRODUCTION: While osteoporosis is common among women of Chinese descent, a readily available bone mineral density (BMD) referent database for Chinese American women does not exist. Fracture risk among this population is currently assessed using a Caucasian reference as well as diagnostic criteria for osteoporosis developed for postmenopausal Caucasian women. Many studies indicate that there are important racial differences in skeletal health and fracture risk, an observation that makes the application of Caucasian data to all groups problematical. This study was undertaken to establish a BMD referent database in Chinese American women and to compare it with a Caucasian female database. It is expected that a race-specific database will be useful in the assessment of bone health for Chinese American women. METHODS: Healthy Chinese American women (n=359), ages 20-90, were recruited. Along with dual-energy X-ray absorptiometry (DXA) of the total hip and lumbar spine, demographic, medical, familial, nutritional, and behavioral data were obtained. The mean and standard deviation for BMD at each site was calculated for each 10-year age group and compared to mean BMD values for Caucasian women supplied as found in the Hologic DXA instrument. Osteoporosis diagnosis rates for this cohort, calculated with the Caucasian and newly established Chinese American BMD referent values, were compared with each other. RESULTS: Compared with Caucasian women, Chinese American women have significantly lower BMD at the lumbar spine, total hip, and femoral neck across a wide spectrum of age groups. As a consequence, more than one-half of Chinese American women>or=50 years of age, who would be characterized as osteoporotic using a Caucasian referent, would not be diagnosed as such if a Chinese American referent were utilized. CONCLUSION: Chinese American reference BMD values are significantly lower than those for Caucasian women. Future studies relating Chinese American BMD values to fracture risk are necessary in order to determine if ethnic database-derived T-scores would be more predictive of fracture risk and to develop meaningful diagnostic criteria for this population.

Absorptiometry, Photon↗
PubMed2006

Databases of free expression.

The rapid development of microarray technologies has led to a similar progression in gene expression analysis methods, gene expression applications, and gene expression databases. Public gene expression databases enable any researcher to examine expression of their favorite genes across a wide variety of samples, download sample data for development of new analysis methods, or answer broad questions about gene expression regulation, among other applications. A wide variety of public gene expression databases exist, and they vary in their content, analysis capabilities, and ease of use. This review highlights the current features and describes examples of two broad categories of mammalian microarray databases: tissue gene expression databases and data warehouses.

Animals↗
PubMed2003

[Documentation in the cardiac catheterization laboratory using electronic databases--experiences in 176 German cath labs].

Due to the introduction of a variety of new features to the German health system, such as a new reimbursement system for inpatient work based on diagnosis-related groups, an obligation to detailed documentation for total quality management, as well as due to the continuing increase in the amount of imaging and other data within invasive cardiology, the use of electronic databases for documentation in the cardiac cath lab is of significant importance. The user friendliness and robustness of the software system for daily clinical practice is crucial for the acceptance of electronic documentation systems by physicians, nurses and technicians. This survey was aimed to explore the current practice and experiences of German cardiac catheterization labs with electronic databases particularly designed for documentation in invasive cardiology, including report generation of cath studies, risk and complication management and logistics for medical material ordering for the cath lab. Of the 176 hospitals and practices having agreed in taking part in this surveillance 165, are currently using an electronic database for administration of medical data and study reports. In 64% of the cath labs, a sub-specialized software system for detailed documentation of the course and the results of an invasive procedure, the human and material resources used, generation of the cath report, and documentation of procedural and post-procedural complications for total quality management is used. The acceptance and satisfaction with the software solutions currently available reveals to be rather inhomogeneous. While user-friendliness and flexibility of a number of software products were positively mentioned, main issues, such as missing hardware of software interfaces with the hospital information system for patient administration, missing stability of several systems, image management too complex and report configuration too inconvenient for daily clinical practice, were criticized. In general, in the light of continuing increase of the amount of clinical and imaging data as well as due to the legal obligation of detailed procedural documentation in all areas of invasive cardiology, a documentation system based on electronic databases bears the potential of an enormous economization of the daily workload of a cardiac cath lab. Prerequisites for the acceptance of such a system in clinical practice is not only the stability and reliability of the system but also the ability to link such a sub-system to existing databases via suitable interfaces and the flexibility of the system for modification of its features to meet the individual requirements of each user.

Adult↗
PubMed2001

The use of a personal digital assistant for wireless entry of data into a database via the Internet.

BACKGROUND: Researchers typically record data on a worksheet and at some later time enter it into the database. Wireless data entry and retrieval using a personal digital assistant (PDA) at the site of patient contact can simplify this process and improve efficiency. METHODS: A surgeon and a nurse coordinator provided the content for the database. The computer programmer created the database, placed the pages of the database on the PDA screen, and researched and installed security measures. RESULTS: Designing the database took 6 months. Meeting Health Insurance Portability and Accountability Act of 1996 (HIPAA) requirements for patient confidentiality, satisfying institutional Information Services requirements, and ensuring connectivity required an additional 8 months before the functional system was complete. CONCLUSIONS: It is now possible to achieve wireless entry and retrieval of data using a PDA. Potential advantages include collection and entry of data at the same time, easy entry of data from multiple sites, and retrieval of data at the patient's bedside.

Databases as Topic↗
PubMed2002

Yeast genomic databases and the challenge of the post-genomic era.

Since the completion of the yeast genome sequence in 1996, three genomic databases, the Saccharomyces Genome Database, the Yeast Proteome Database, and MIPS (produced by the Munich Information Center for Protein Sequences), have organized published knowledge of yeast genes and proteins onto the framework of the genome. Now, post-genomic technologies are producing large-scale datasets of many types, and these pose new challenges for knowledge integration. This review first examines the structure and content of the three genomic databases, and then draws from them and other resources to examine the ways knowledge from the literature, genome, and post-genomic experiments is stored, integrated, and disseminated. To better understand the impact of post-genomic technologies, 20 collections of post-genomic data were analyzed relative to a set of 243 previously uncharacterized genes. The results indicate that post-genomic technologies are providing rich new information for nearly all yeast genes, but data from these experiments is scattered across many Web sites and the results from these experiments are poorly integrated with other forms of yeast knowledge. Goals for the next generation of databases are set forth which could lead to better access to yeast knowledge for yeast researchers and the entire scientific community.

Databases, Genetic↗
PubMed2004

The European Network of Health Economic Evaluation Databases (EURO NHEED) Project.

This paper provides a first outline of the European Network of Health Economic Evaluation Databases (EURO NHEED) project. The project is funded by the European Commission and will implement, in 7 European centres based in France, Germany, Italy, The Netherlands, Spain, Sweden and the United Kingdom, databases on the economic evaluation of healthcare interventions. The network will be based on two existing and well-established resources, namely the UK's NHS Economic Evaluation Database (NHS EED), and France's Connaissances et Décision en EConomie de la Santé (CODECS) database. EURO NHEED will initially cover 17 European countries and will provide its users with bibliographic records, detailing the main characteristics of all included studies. In addition, structured abstracts will be provided for articles identified as full economic evaluations (cost-benefit, cost-effectiveness or cost-utility), which will offer a detailed critique of the findings and the methodology used. These databases will be accessible free of charge on the Internet. The EURO NHEED project is the first attempt to develop such a resource on a multi-national basis. The project will bring together Health Economists and Information Scientists from the European Union and beyond and is anticipated to facilitate a number of benefits and advances in the field of Health Economics. These include harmonisation and increased understanding of the theory and methodology of economic evaluation in healthcare, the interpretation of the generalisability of studies to target settings, and the influence of healthcare system variations among the European countries. The project will therefore advance the state of the art in collecting, summarising, critiquing and disseminating economic evaluations of healthcare conducted within Europe.

Cost-Benefit Analysis↗
PubMed2004

Strategies for consulting with the community: the cases of four large-scale genetic databases.

Large-scale genetic databases are being developed in several countries around the world. However, these databases depend on public participation and acquiescence. In the past, information campaigns have been waged and little attention has been paid to dialogue. Nowadays, it is important to include the public in the development of scientific research and to encourage a free, open and useful dialogue among those involved. This paper is a review of community consultation strategies as part of four proposed large-scale genetic databases in Iceland, Estonia, United Kingdom and Quebec. The Iceland Health Sector Database and Estonian Genome Project have followed a "communication approach" in order to address public concerns, whereas, UK Biobank and Quebec CARTaGENE have chosen a "partnership approach" to involve the public in decision-making processes. Following a comparison of community consultation strategies, the main concerns of the public are examined as well as the challenges of involving communities. Importantly, reported across all groups is the concern for confidentiality, respect of the individual, transparency, and the donor's right to access to their own result. However, even if researchers demonstrate a willingness to respect values such as fair representation, transparency and accountability, there is still a risk that the public will mistrust researchers and simply will not participate in sufficient numbers. Complications may arise when individual and community interests conflicts. The implementation of a partnership approach is definitely involving and costly; however, if used properly, this method can improve both participation and so database development.

Community Participation↗
PubMed1994

Coronary artery bypass grafting: the Society of Thoracic Surgeons National Database experience.

The need for accurate risk assessment has become an indispensable element in the practice of cardiac surgery. The Society of Thoracic Surgeons National Cardiac Surgery Database allows subscribing institutions to perform sophisticated patient risk assessment using traditional statistical tools and a newly developed risk model of operative mortality. The database experience with isolated coronary artery bypass grafting has been studied most closely at this point and serves as the basis for this report. The approach to operative risk assessment is presented along with an analysis of important risk factors in the practice of coronary artery surgery from 1980 through 1990. The database contains records of 80,881 patients undergoing coronary artery bypass grafting in numerous institutions from 1980 through 1990. These records were used to conduct a detailed analysis of risk factors associated with coronary operations in this time interval and to present statistical methods used to formulate a risk equation that allows one to predict the probability of operative death. In the course of this decade, there were clearly defined trends showing a statistically significant increase in adverse patient risk factors. The risk model has proven to be a reliable tool for predicting the probability of operative death in an individual patient and may be valuable in both patient counseling and medical decision making. Large multi-institutional databases of this type are key ingredients of modern operative risk assessment. A database containing a broad national experience of this type can represent an aggregate experience that may well approximate a universally accepted standard of care.

Adult↗
PubMed1994

A deductive database system for analyzing human nucleotide sequence data.

The analysis of the human genome is one of the most significant topics in both biology and medical science. There is a growing need for a well-designed database system for searching and analyzing the human genome data. We developed a deductive database system to search and analyze nucleotide sequence data derived from the GenBank primates data. A deductive database system is a next generation one and it contains an inference mechanism that can handle problems beyond the capabilities of classical database systems. Database queries are described in logical rules. These rules are simple even for molecular biologists who are not experts in computer programs because they are declarative and do not require the procedural commands that are usually used in computer programs. Furthermore, queries based on logical rules are powerful enough to express complicated biological problems. Particularly, recursive rules are suitable for examining secondary structures of nucleotide sequences. In our analysis of TfR's IRE, we noted five stem-and-loop structures.

Artificial Intelligence↗
PubMed2004

Protein sequence databases.

A variety of protein sequence databases exist, ranging from simple sequence repositories, which store data with little or no manual intervention in the creation of the records, to expertly curated universal databases that cover all species and in which the original sequence data are enhanced by the manual addition of further information in each sequence record. As the focus of researchers moves from the genome to the proteins encoded by it, these databases will play an even more important role as central comprehensive resources of protein information. Several the leading protein sequence databases are discussed here, with special emphasis on the databases now provided by the Universal Protein Knowledgebase (UniProt) consortium.

Animals↗