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PubMed1995

The Protein Disease Database of human body fluids: II. Computer methods and data issues.

The Protein Disease Database (PDD) is a relational database of proteins and diseases. With this database it is possible to screen for quantitative protein abnormalities associated with disease states. These quantitative relationships use data drawn from the peer-reviewed biomedical literature. Assays may also include those observed in high-resolution electrophoretic gels that offer the potential to quantitate many proteins in a single test as well as data gathered by enzymatic or immunologic assays. We are using the Internet World Wide Web (WWW) and the Web browser paradigm as an access method for wide distribution and querying of the Protein Disease Database. The WWW hypertext transfer protocol and its Common Gateway Interface make it possible to build powerful graphical user interfaces that can support easy-to-use data retrieval using query specification forms or images. The details of these interactions are totally transparent to the users of these forms. Using a client-server SQL relational database, user query access, initial data entry and database maintenance are all performed over the Internet with a Web browser. We discuss the underlying design issues, mapping mechanisms and assumptions that we used in constructing the system, data entry, access to the database server, security, and synthesis of derived two-dimensional gel image maps and hypertext documents resulting from SQL database searches.

Body Fluids↗
PubMed2004

The contact allergen replacement database and treatment of allergic contact dermatitis.

OBJECTIVE: To determine whether the Contact Allergen Replacement Database would improve clinical outcomes for patients with allergic contact dermatitis associated with topical skin care products by helping patients avoid known allergens. DESIGN: This study was a randomized, single-blind, controlled trial. SETTING: The study was conducted at the outpatient facilities at Mayo Clinic, Scottsdale, Ariz, and Rochester, Minn. PARTICIPANTS: Of the 29 patients enrolled, 21 completed the study. INTERVENTION: All patients were randomly assigned to either a Contact Allergen Replacement Database group or a traditional therapy group. Patients in the database group received an individualized list of topical skin care products free of the antigens identified by the results of their individual patch tests. Otherwise, the 2 groups received identical therapy. MAIN OUTCOME MEASURES: To evaluate erythema, scale, and pruritus at 3-month follow-up, each variable was given a severity score from 0 to 3. A 1-point change was considered clinically notable. We also evaluated total physician-patient counseling time and patient satisfaction. RESULTS: We found no statistically significant differences (P>.05) between the 2 treatment groups on measures of disease activity and counseling time. However, 91% of the database group reported the allergen-free product list to be either somewhat helpful or very helpful in managing contact dermatitis. All the patients without access to the database said it would have been helpful. CONCLUSIONS: Although this small study, with its limited follow-up, did not yield objective evidence supporting the use of the Contact Allergen Replacement Database, the database-generated product lists were favorably received by patients. We anticipate an expanded clinical role for this database as an Internet-based resource.

Administration, Topical↗
PubMedDate not supplied

Thermodynamic databases for proteins and protein-nucleic acid interactions.

Thermodynamic data regarding proteins and their interactions are important for understanding the mechanisms of protein folding, protein stability, and molecular recognition. Although there are several structural databases available for proteins and their complexes with other molecules, databases for experimental thermodynamic data on protein stability and interactions are rather scarce. Thus, we have developed two electronically accessible thermodynamic databases. ProTherm, Thermodynamic Database for Proteins and Mutants, contains numerical data of several thermodynamic parameters of protein stability, experimental methods and conditions, along with structural, functional, and literature information. ProNIT, Thermodynamic Database for Protein-Nucleic Acid Interactions, contains thermodynamic data for protein-nucleic acid binding, experimental conditions, structural information of proteins, nucleic acids and the complex, and literature information. These data have been incorporated into 3DinSight, an integrated database for structure, function, and properties of biomolecules. A WWW interface allows users to search for data based on various conditions, with different display and sorting options, and to visualize molecular structures and their interactions. These thermodynamic databases, together with structural databases, help researchers gain insight into the relationship among structure, function, and thermodynamics of proteins and their interactions, and will become useful resources for studying proteins in the postgenomic era.

DNA↗
PubMed2006

The cypriot and Iranian National Mutation Frequency Databases.

The National Mutation Frequency Databases are continuously updated mutation depositories, which contain extensive information over the described genetic heterogeneity of an ethnic group or population. Here, we report the construction of the Cypriot (http://www.goldenhelix.org/cypriot) and Iranian National Mutation Frequency Databases (http://www.goldenhelix.org/iranian), both derived from an academic effort to provide high quality and up-to-date information on the underlying genetic heterogeneity of inherited disorders in the Cypriot and Iranian populations, respectively. Both databases have been built and maintained online using ETHNOS platform, a specialized software, which provides the means for national mutation database construction and curation. Each database contains brief summaries of the various genetic disorders studied for each population, and an easy-to-use query interface provides, both to specialist as well as to non-specialist users (i.e. patients and their families), instant access to the list and frequencies of the different mutations responsible for the inherited disorders in these populations. Furthermore, numerous links to the respective Online Mendelian Inheritance in Man (OMIM) entries and, when available, to the locus-specific databases fruitfully integrate the databases content into a single Web site. Both databases can serve as valuable online tools for molecular genetic testing of inherited disorders in these populations and could potentially motivate further investigations of yet unknown genetic diseases in the Cypriot and Iranian populations.

Cyprus↗
PubMedDate not supplied

Using databases for studying and comparing health care costs and resource use.

Data sources such as medical insurance claims are increasingly used in health outcomes research. We present opportunities and limitations associated with the use of such data for conducting studies of health care costs and resource use. We also provide examples on using databases for conducting research when the primary objective is to study costs or resource use. This information is intended to be helpful to experienced health services researchers and to those new to the field of either outcomes research or cost effectiveness research. We examine the reasons for using databases to study costs and resource use, desirable attributes of databases used for this purpose, potential pitfalls, other issues associated with conducting cost and resource use studies with databases, and appropriate methods for this research. Through examples and references, we examine issues to be considered in each of these areas, and make recommendations. Strengths and limitations of databases are indicated. Research using claims data to determine health care cost and resource use should be carried out responsibly. Limitations must be acknowledged for research using databases, and appropriate methods must be used. Still, databases represent a rich opportunity to conduct research in health care costs and resource use, and much can be learned using databases.

Databases as Topic↗
PubMed1994

Derivation of rules for comparative protein modeling from a database of protein structure alignments.

We describe a database of protein structure alignments as well as methods and tools that use this database to improve comparative protein modeling. The current version of the database contains 105 alignments of similar proteins or protein segments. The database comprises 416 entries, 78,495 residues, 1,233 equivalent entry pairs, and 230,396 pairs of equivalent alignment positions. At present, the main application of the database is to improve comparative modeling by satisfaction of spatial restraints implemented in the program MODELLER (Sali A, Blundell TL, 1993, J Mol Biol 234:779-815). To illustrate the usefulness of the database, the restraints on the conformation of a disulfide bridge provided by an equivalent disulfide bridge in a related structure are derived from the alignments; the prediction success of the disulfide dihedral angle classes is increased to approximately 80%, compared to approximately 55% for modeling that relies on the stereochemistry of disulfide bridges alone. The second example of the use of the database is the derivation of the probability density function for comparative modeling of the cis/trans isomerism of the proline residues; the prediction success is increased from 0% to 82.9% for cis-proline and from 93.3% to 96.2% for trans-proline. The database is available via electronic mail.

Amino Acid Sequence↗
PubMed2003

Establishment and evaluation of bone mineral density reference databases appropriate for diagnosis and evaluation of osteoporosis in Chinese women.

This study was designed to establish Bone Mineral Density (BMD) Reference Databases for multiple skeletal sites appropriate for the diagnosis and evaluation of osteoporosis (OP) in Chinese women. We recruited 2702 healthy Chinese women, 5-96 years of age, for BMD assessment. BMD values at multiple skeletal sites including anteroposterior (AP) and lateral (Lat) lumbar spine, hip, and forearm were measured by dual-energy X-ray absorptiometry (DXA) using a QDR 4500A device; results were analyzed according to age group using eight regression models. BMD Reference Databases (CWD) were established according to the best regression equation and compared with Hologic reference databases for "Oriental Women" (OWD). Results indicated that the cubic regression model was superior to the quadratic, linear, logarithmic, and exponential regression models, etc. for our purpose, with a determinate coefficient ( R(2)) of 0.363-0.650 ( P = 0.000). We included 1636 female patients, aged 35-86 years, in our tests. In comparison with Hologic Reference Databases, the mean detection rate of OP in the newly established BMD Reference Databases for Chinese Women (CWD) was 16.0% +/- 2.68% lower (range, 13.7%-20.5%) at the AP spine, 16.8% +/- 11.0% lower (range, 3.5%-32.8%) at the Lat spine (except for L4), 18.7% +/- 4.6% lower (range, 12.6%-24.2%) at the hip, and 14.3% +/- 6.9% higher (range, 4.7%-24.3%) at the forearm. The difference in detection rates for OP was significant between the two reference databases ( P = 0.000), which was consistent with the differences in peak BMD values and the biological variability between them. Based upon our data, we confirmed that the Hologic BMD Reference Databases for Oriental Women (OWD) were not suitable for the diagnosis of OP in Chinese women; the BMD Reference Databases for Chinese Women (CWD) established in this study would provide reliable diagnostic standards for detection of OP in the women of South China.

Adolescent↗
PubMed2005

BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures.

We present two new databases of NMR-derived distance and dihedral angle restraints: the Database Of Converted Restraints (DOCR) and the Filtered Restraints Database (FRED). These databases currently correspond to 545 proteins with NMR structures deposited in the Protein Databank (PDB). The criteria for inclusion were that these should be unique, monomeric proteins with author-provided experimental NMR data and coordinates available from the PDB capable of being parsed and prepared in a consistent manner. The Wattos program was used to parse the files, and the CcpNmr FormatConverter program was used to prepare them semi-automatically. New modules, including a new implementation of Aqua in the BioMagResBank (BMRB) software Wattos were used to analyze the sets of distance restraints (DRs) for inconsistencies, redundancies, NOE completeness, classification and violations with respect to the original coordinates. Restraints that could not be associated with a known nomenclature were flagged. The coordinates of hydrogen atoms were recalculated from the positions of heavy atoms to allow for a full restraint analysis. The DOCR database contains restraint and coordinate data that is made consistent with each other and with IUPAC conventions. The FRED database is based on the DOCR data but is filtered for use by test calculation protocols and longitudinal analyses and validations. These two databases are available from websites of the BMRB and the Macromolecular Structure Database (MSD) in various formats: NMR-STAR, CCPN XML, and in formats suitable for direct use in the software packages CNS and CYANA.

Databases, Protein↗
PubMedDate not supplied

An object-based architecture for biomedical expert database systems.

Objects play a major role in both database and artificial intelligence research. In this paper, we present a novel architecture for expert database systems that introduces an object-based interface between relational databases and expert systems. We exploit a semantic model of the database structure to map relations automatically into object templates, where each template can be a complex combination of join and projection operations. Moreover, we arrange the templates into object networks that represent different views of the same database. Separate processes instantiate those templates using data from the base relations, cache the resulting instances in main memory, navigate through a given network's objects, and update the database according to changes made at the object layer. In the context of an immunologic-research application, we demonstrate the capabilities of a prototype implementation of the architecture. The resulting model provides enhanced tools for database structuring and manipulation. In addition, this architecture supports efficient bidirectional communication between database and expert systems through the shared object layer.

Database Management Systems↗
PubMed2005

The CORRONA database.

BACKGROUND: Large, long-term databases are needed in order to provide information on the safety and efficacy of new agents used in the treatment of rheumatoid arthritis (RA) and psoriatic arthritis (PsA). These databases can provide data which is well beyond what is available from industry-sponsored investigations. METHODS: The structure, governance, content, context and developmental plan of the CORRONA database are described. RESULTS: The CORRONA database has grown from start up in 2002 to the largest independent database in North America which collects data from both rheumatologists and patients at the time of a clinical encounter. Data are collected as often as every 3 months in RA and every 6 months in PsA. As of the time of this writing, the CORRONA database consists of approximately 9000 patients with RA and 1000 with PsA. Data can be used to elucidate toxicities found in frequencies which would be considerably less common than can be uncovered in industry-sponsored investigations. In addition, actual prescribing patterns and responses in clinical practice can be investigated and described. CONCLUSION: After 3 years of data collection, the CORRONA database is now appropriately able to make significant contributions to our understanding of the safety, efficacy of drugs, as well as demographic, and socioeconomic profiles of patients with RA and PsA. It has evolved from a nascent database to a mature one poised to make significant contributions.

Antirheumatic Agents↗
PubMed2006

Comparative evaluation of local and international reference databases for forearm densitometry: different impacts on diagnostic decisions.

Reference databases play a key role in the management of osteoporosis. The aim of this preliminary study was to compare the diagnostic consequences of using either an international or a local reference database in peripheral densitometry. For this purpose, standard curves for bone mineral density (measured by dual-energy X-ray absorptiometry at the distal and proximal forearm) were generated for healthy Hungarian men and women. In total, 303 healthy volunteers of both sexes (age range: 20-94 yr) were recruited from four osteoporosis centers. Subjects with medical conditions or taking medication affecting the bone metabolism were excluded. Bone densitometry was performed with pDEXA (Norland-Stratec, Fort Atkinson, WI) devices in each center after cross-calibration of the machines. The precision error of the forearm measurement was also determined (<1% in vitro, and 1.2-2.5% in vivo). In females, the peak forearm density was detected in the 30-39-yr group. The density decreased by 8% per 5 yr in early postmenopausal females, and by 10% per 10 yr in late postmenopausal females. In males, the highest bone mineral density was found in the 30-39-yr group for the distal forearm, but 1 decade later for the proximal site. Subsequently, a 5% decrease in density occurred per 10 yr, except in the 8th decade, in which a 20% decrease was demonstrated. One thousand four hundred thirty-four patients with suspected osteoporosis were classified according to the forearm density T-scores using both the new Hungarian reference database and the international database provided by the manufacturer. Comparison of the results measured at the distal forearm with the two different databases led to similar outcomes. However, at the proximal site, one fifth of the female patients were reclassified from the low-density group to the normal group using the domestic normative database. An opposite difference was observed for the males: use of the Hungarian reference data resulted in 40% more men being categorized in the low-density group than when the international normal database was applied. Our results suggest that not only geographic differences, but also the reference database used, can influence the prevalence of the diagnosis of osteoporosis. Further data are currently being collected to increase the statistical power of the study.

Absorptiometry, Photon↗
PubMed2005

Does reporting of coronary artery bypass grafting from administrative databases accurately reflect actual clinical outcomes?

OBJECTIVES: Quality assessment of coronary artery bypass grafting has traditionally been performed with data from clinical databases. Administrative databases that rely primarily on information collected for billing purposes increasingly have been used as tools for public reporting of outcomes quality. The correlation of administrative data with clinical data for clinical quality assessment has not been confirmed. METHODS: With data from a clinical database, we analyzed the outcomes of all patients who underwent coronary artery bypass grafting surgery in 1 hospital between 1999 and 2001. This information was collected before, during, and after the surgery and hospitalization by designated clinical individuals involved with the patient's care and then entered into an audited clinical database (The Society of Thoracic Surgeons National Cardiac Database). These data were then compared with administrative data collected on the same cohort of patients for the number of procedures performed and mortality rate as reported by the federal government (Medical Provider Analysis and Review), state government (Texas Health Care Information Council), hospital system (HCA, Inc, Casemix Database), and an internet Web site (healthgrades.com). Data were analyzed on the basis of the population reported, definitions used, risk assessment algorithms, and case volumes. RESULTS: By using the audited The Society of Thoracic Surgeons database as the standard and aggregating the reporting of case volumes by the inclusion criteria of various sources of administrative data, we found variances in the reported procedure volumes and mortality. Case volumes were overreported by as much as 21% in all patients and underreported by up to 16% or more in Medicare patients. Mortality in administrative data exceeded that reported in clinical data by 21%. Reasons for variances included time period reported (calendar vs fiscal year), population reported (all patients, Medicare patients, Medicare patients aged >/= 65 years), date used for the patient record captured (date of surgery, discharge), and the definition of mortality. Different proprietary risk-adjusting algorithms used magnified variances with risk-adjusted mortality exceeding the Society of Thoracic Surgeons data by as much as 61%. CONCLUSIONS: Substantial variability of reported outcomes is seen in administrative data sets compared with an audited clinical database in the end points of the number of procedures performed and mortality. This variability makes it challenging for the nonclinician unfamiliar with outcomes analysis to make an informed decision.

Aged↗
PubMed2004

NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database.

Compound identification and support for computer-assisted structure elucidation via a free community-built web database for organic structures and their NMR data is described. The new database NMRShiftDB is available on . As the first NMR database, NMRShiftDB allows not only open access to the database but also open and peer reviewed submission of datasets, enabling the natural products community to build its first free repository of assigned 1H and 13C NMR spectra. In addition to the open access, the underlying database software is built solely from free software and is available under an open source license. This allows collaborating laboratories to fully replicate the database and to create a highly available network of NMRShiftDB mirrors. The database contains about 10,000 structures and assigned spectra, with new datasets constantly added. Its functionality includes (sub-) spectra and (sub-) structure searches as well as shift prediction of 13C spectra based on the current database material.

Databases, Factual↗
PubMed1999

Comparison of 4 nutrient databases with chemical composition data from the Dietary Approaches to Stop Hypertension trial. DASH Collaborative Research Group.

Accuracy of computerized nutrient databases is an important consideration in selecting a nutrient analysis system. We project compared the nutrient content of daily menus calculated from 4 microcomputer programs to chemical analysis of menus analyzed for the Dietary Approaches to Stop Hypertension (DASH) trial. Thirty-six menus were entered at 2 independent DASH sites using the ESHA Food Processor, Minnesota Nutrition Data System, Moore's Extended Nutrient Database, and Nutritionist IV databases. Food prepared according to these menus was chemically analyzed at the Food Analysis Laboratory Control Center at Virginia Polytechnic Institute and State University, Department of Biochemistry, Blacksburg. Estimates for 13 nutrients were compared: energy, total fat, saturated fat, monounsaturated fat, polyunsaturated fat, carbohydrate, protein, cholesterol, calcium, potassium, magnesium, iron, and sodium. The overall intraclass correlation between the 2 sites' data entry was 0.998; thus, values were averaged for analyses. Databases varied significantly in their mean deviations from chemical analyses values for saturated, monounsaturated, and polyunsaturated fatty acids, potassium, magnesium, and iron (P < .05); however, these differences were small (< 10%). Absolute deviations, which estimate the combined effect of bias and precision, were significantly different among databases for energy, saturated fatty acids, and polyunsaturated acids. Absolute differences from the laboratory values varied by < 15%, except for iron. All 4 databases were comparable in accuracy and precision and performed well. Criteria for database selection depends not only on overall database accuracy, especially for nutrients of interest, but also on the ease of use of the program, relevant features of the associated software; and cost.

Blood Pressure↗
PubMed1996

Issues in designing a student database.

Many larger colleges of nursing have centralized student databases in which all elements of students' records are collated. The smaller department or college may leave the design of such databases to course leaders. This paper highlights stages and considerations in the development of student databases. It offers definitions of flat-file and relational databases; it identifies issues in prior planning and then of direct plannings of the database. It offers a discussion of a number of issues related to what sort of information is stored in a student database. It closes with a discussion of the training needs of those staff who are going to use such a database. The principles described in this paper can also be adapted for use in the designing of any health care related database system. The paper also addresses the question of why all colleges are not, already, using such systems.

Computer User Training↗
PubMed2006

[Comparison of the French DRG based information system (PMSI) with the National Mesothelioma Surveillance Program database].

BACKGROUND: One of the main purposes of the French National Mesothelioma Surveillance Program is to estimate and follow the national incidence of pleural mesothelioma. We wanted to study the contribution of the French hospital national database as a valid source of mesothelioma incident cases. METHODS: From the 1998 and 1999 hospital national database, medical records with a diagnosis code of mesothelioma or pleural cancer where selected among patients who resided in one of the 17 administrative divisions covered by the National Mesothelioma Surveillance Program in 1998. From these records, 506 patients in 1998 and 474 patients in 1999 where identified and matched with the National Mesothelioma Surveillance Program cases over the same period using indirect criteria of identification (sex, age, place of residence). Medical records of cases unknown by the National Mesothelioma Surveillance Program where consulted in one of the administrative divisions. RESULTS: Only two-thirds of the registered cases of the National Mesothelioma Surveillance Program could be matched with a patient identified in the hospital national database with a diagnosis of mesothelioma registered during the same year. Consultation of the medical records showed that 1) certified cases registered in the National Mesothelioma Surveillance Program where often (83%) found in the hospital national database with a code of mesothelioma but 10 to 15% of the patients with a code of mesothelioma in the national hospital databases had a different diagnosis according to their medical records; 2) 65% of the patients with a code of mesothelioma in the national hospital databases that where unknown from the National Mesothelioma Surveillance Program in 1998 and 55% in 1999 where prevalent cases; 3) 3 suspected cases had not been reported to the National Mesothelioma Surveillance Program. CONCLUSION: Because of lack of diagnosis certification, mistakes in encoding diagnosis and the fact that incident and prevalent cases cannot be distinguished in the hospital national database make it impossible to estimate the mesothelioma incidence solely from this source of data. However, the hospital claim databases constitute a complementary source of information for the active search of incident cases performed by the National Mesothelioma Surveillance Program.

Databases, Factual↗
PubMed1997

Evaluating the options for developing databases to support research-based medicine at the NHS Centre for Reviews and Dissemination.

The paper presents the results of a questionnaire survey and user interface review group experiments to determine the value and ease of use of the Database of Abstracts of Reviews of Effectiveness (DARE) and the NHS Economic Evaluations Database (NEED). The results are interpreted with other recent studies of the use of electronic databases, including the NHS Research Register User Requirements Specification. The study found that most frequent users of the DARE database tend to use the CD-ROM version. Librarians were found to have the greatest awareness of the databases, with relatively low levels of use by operational NHS Staff. Untrained users found the online databases difficult to access and had erroneous perceptions of the database content which were only realised when queries returned unexpected answers. Experienced users of online information systems tended to want more sophisticated search facilities than inexperienced users. Nearly all users in the review groups wanted to access the databases in conjunction with other information sources, such as the Cochrane Library, Medline and the ACP Journal Club, highlighting the need for cross organisational strategies for the dissemination of research-based information.

CD-ROM↗
PubMed2002

Mass spectrometric methods for generation of protein mass database used for bacterial identification.

The availability of a suitable database is critical in a proteomic approach for bacterial identification by mass spectrometry (MS). The major limitation of the present public proteome database is the lack of extensive low-mass bacterial protein entries with masses experimentally verified for most bacteria. Here, we present a method based on mass spectrometry to create protein mass tables specifically tailored for bacterial identification. Several issues related to the detection of bacterial proteins for the purpose of database creation are addressed. Three species of bacteria, namely, Escherichia coli, Bacillus megaterium, and Citrobacter freundii, which can be found in the ambient environment, were chosen for this study. Direct matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS analysis of each bacterial extract reveals 20-29 protein components in the mass range from 2000 to 20,000 Da. HPLC fractionation of bacterial extracts followed by off-line MALDI-TOF analysis of individual fractions detects 156-423 components. Analysis of the extracts by HPLC/electrospray ionization MS shows the number of detectable proteins in the range of 46-59. Although a number of components were common to the three detection schemes employed, some unique components were found using each of these techniques. In addition, for E. coli where a large proteome database exists in the public domain, a number of masses detected by the mass spectrometric methods do not match with the proteome database. Compared to the public proteome database, the mass tables generated in this work are demonstrated to be more useful for bacterial identification in an application where the bacteria of interest have limited protein entries in the public database. The implication of this work for future development of a comprehensive mass database is discussed.

Bacteria↗