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Mediator-lipidomics: databases and search algorithms for PUFA-derived mediators.

Lipid mediators (LMs) derived from PUFAs play important roles in health and disease. Databases and search algorithms are crucial, but currently unavailable, for accurate and prompt analysis of LMs via liquid chromatography-ultraviolet-tandem mass spectrometry (LC-UV-MS/MS). A novel algorithm and databases, cognoscitive-contrast-angle algorithm and databases (COCAD), were developed for the identification of LMs based on the integration of standard MS/MS spectra with chromatograms and UV spectra. Segment naming and empirical fragmentation rules were introduced to determine MS/MS ion identities, along with ion intensities used by COCAD in matching the unknown to those of authentic standards. The structures of potential LMs without synthetic and/or authentic products as standards were identified by developing theoretical databases and algorithms based on virtual LC-UV-MS/MS spectra and chromatograms. The performance of these databases and algorithms was tested by identifying LMs in murine tissues. These results indicate that COCAD has many advantages for profiling and identification of LMs compared with the conventional dot-product algorithm.

Algorithms↗

Database development in toxicogenomics: issues and efforts.

The marriage of toxicology and genomics has created not only opportunities but also novel informatics challenges. As with the larger field of gene expression analysis, toxicogenomics faces the problems of probe annotation and data comparison across different array platforms. Toxicogenomics studies are generally built on standard toxicology studies generating biological end point data, and as such, one goal of toxicogenomics is to detect relationships between changes in gene expression and in those biological parameters. These challenges are best addressed through data collection into a well-designed toxicogenomics database. A successful publicly accessible toxicogenomics database will serve as a repository for data sharing and as a resource for analysis, data mining, and discussion. It will offer a vehicle for harmonizing nomenclature and analytical approaches and serve as a reference for regulatory organizations to evaluate toxicogenomics data submitted as part of registrations. Such a database would capture the experimental context of in vivo studies with great fidelity such that the dynamics of the dose response could be probed statistically with confidence. This review presents the collaborative efforts between the European Molecular Biology Laboratory-European Bioinformatics Institute ArrayExpress, the International Life Sciences Institute Health and Environmental Science Institute, and the National Institute of Environmental Health Sciences National Center for Toxigenomics Chemical Effects in Biological Systems knowledge base. The goal of this collaboration is to establish public infrastructure on an international scale and examine other developments aimed at establishing toxicogenomics databases. In this review we discuss several issues common to such databases: the requirement for identifying minimal descriptors to represent the experiment, the demand for standardizing data storage and exchange formats, the challenge of creating standardized nomenclature and ontologies to describe biological data, the technical problems involved in data upload, the necessity of defining parameters that assess and record data quality, and the development of standardized analytical approaches.

Animals↗

Full-text and bibliographic database searching in the health sciences: an exploratory study comparing CCML and MEDLINE.

An exploratory study to investigate perceived differences between searching full-text databases and bibliographic databases was undertaken. BRS's full-text database, Comprehensive Core Medical Library (CCML), and BRS's current MEDLINE file (MESH) were compared. Identical literature search topics were run in the two databases and the results evaluated regarding currency of search results, success in answering specific questions, uniqueness of information retrieved, and relevancy of retrieval. Additionally, connect time and costs were noted to aid in determining the feasibility of offering full-text database searching as a service for which the authors' institution would charge.

Data Collection↗

Pharmaceutical published literature databases: a survey.

Pharmaceutical companies often maintain a bibliographic database of published articles on their products. Although such databases share the common purpose of providing the company with a centralized source of published information, the databases themselves vary in scope, uses, and technologies. In order to explore the current status of these databases, a survey was conducted in early 1995. This article provides an overview of pharmaceutical product literature databases and the results from that survey.

Databases, Bibliographic↗

Global health database.

The Global Health database is available from Ovid Technologies, Inc., and also from CABI Publishing, EBSCO, and DataStar/ DIALOG. This database is really the combination of two others--the Public Health and Tropical Medicine database, formerly produced by the Bureau of Hygiene and Tropical Diseases, as well as human health and diseases information that is extracted from the CAB Abstracts database. This column will provide readers with an overview of the Global Health database, as well as present some searching hints. The Ovid interface will be used.

Databases as Topic↗

Recalculation of the NHANES database SD improves T-score agreement and reduces osteoporosis prevalence.

UNLABELLED: In attempt to improve diagnostic agreement between manufacturers, a recent software update incorporated NHANES III data in GE Lunar densitometers. As a result, the femur neck and trochanter T-scores were lowered, and osteoporosis prevalence was increased. Use of a recalculated young-normal SD for the GE Lunar-adjusted NHANES III database improved diagnostic agreement and is recommended. INTRODUCTION: Use of manufacturer-specific normative databases for T-score derivation leads to discordance in T-score values and differences in diagnostic classification. To address this issue, the International Committee for Standards in Bone Measurement (ICSBM) recommended the NHANES III database for femur T-score derivation. Acquired on Hologic (Hol) instruments, this database requires conversion equations for application to other DXA systems. NHANES III total femur (TF) conversions for GE Lunar (GE) have previously been available, and femoral neck (FN) and trochanter (TR) equations were reported recently. Per the ICSBM recommendation, GE Lunar incorporated these values into their female database. This should produce T-score and diagnostic agreement between Hol and GE instruments; however, this has not been evaluated. MATERIALS AND METHODS: We compared GE femur scans in 115 postmenopausal women using software before and after the NHANES III software update. Subsequently, T-scores derived from femur scans obtained on GE and Hol densitometers were compared in a different group of 89 postmenopausal women. RESULTS: The NHANES III software update had no effect on measured BMD (g/cm2) at any femur region. However, because of changes in values used for T-score calculation (increase in the mean young-normal BMD at the FN and TR and a reduction in SD at the TR), the T-scores were lower (mean, 0.48 and 0.68, respectively) at the FN and TR using post-NHANES III software. Consequently, this update increased femur osteoporosis prevalence in these 115 women from 7.8% to 18.3%. Comparison of GE with Hol total proximal femur T-scores revealed a minimal difference (<0.1) and equal diagnoses of osteoporosis. FN and TR differences were larger, with mean GE T-scores lower than Hol (p < 0.001) by 0.17 and 0.50, respectively, thereby introducing osteoporosis diagnostic disagreement (13 [GE] versus 9 [Hol]). Our evaluation suggested that this disparity resulted from direct application of published NHANES III SDs at the FN and TR. As such, we applied the conversion formulae to the NHANES III published Hologic data and found the FN and TR SDs were greater than assumed by GE. Using our recalculated SD to derive T-scores reduced the mean GE/Hol T-score difference to 0.03 at the FN and 0.32 at the TR and resolved osteoporosis diagnostic disagreement. CONCLUSION: The GE NHANES III software update leads to lower FN and TR T-scores than obtained with Hol or prior GE software. Recalculation of the young-normal SD reduces this difference and is recommended. Clinicians are advised to avoid using the TR for diagnosis or, at a minimum, use caution when making treatment decisions based solely on T-score at this site.

Absorptiometry, Photon↗

Vaccine safety surveillance using large linked databases: opportunities, hazards and proposed guidelines.

Combined administrative databases are referred to as 'large linked databases' because of their relatively large size and the need for linkage of different data sets that were created separately from each other. Such linked databases have become popular in vaccine safety surveillance. Whereas their use offers some unique opportunities, their increasingly widespread use can also lead to wrongful linkage of vaccines to adverse events. We review the opportunities and hazards of using large linked databases for vaccine safety surveillance and propose some guidelines to increase the reliability of the outcomes. We also offer our opinion on the future use of large linked databases for vaccine safety surveillance purposes.

Adverse Drug Reaction Reporting Systems↗

Development of an integrated stroke outcomes database within Veterans Health Administration.

A fundamental goal of the Rehabilitation Outcomes Research Center of Excellence is to improve care and outcomes for veterans with rehabilitation needs. To achieve this goal, the Center's primary objective is increasing research capacity. The Integrated Stroke Outcomes Database is a collection of Veterans Health Administration (VHA) clinical and administrative data containing patient information on a cohort of stroke patients found in the Functional Status Outcomes Database (FSOD), National Patient Care Database (NPCD), and other VHA sources. Clinical and administrative data were abstracted from several VHA data sources and linked to form an integrated outcomes database. A primary cohort of stroke patients treated during fiscal year (FY) 2001 was identified from the FSOD. Matching data from the NPCD, Decision Support System, Health Economics Resource Center, and the National Veterans Survey were obtained, merged, and reported in brief. This integrated database structure will provide valuable support to enhance the VHA capacity to perform stroke rehabilitation research.

Ambulatory Care↗

An integrated database of the ascidian, Ciona intestinalis: towards functional genomics.

An integrated genome database is essential for future studies of functional genomics. In this study, we update cDNA and genomic resources of the ascidian, Ciona intestinalis, and provide an integrated database of the genomic and cDNA data by extending a database published previously. The updated resources include over 190,000 ESTs (672,396 in total together with the previous ESTs) and over 1,000 full-insert sequences (6,773 in total). In addition, results of mapping information of the determined scaffolds onto chromosomes, ESTs from a full-length enriched cDNA library for indication of precise 5'-ends of genes, and comparisons of SNPs and indels among different individuals are integrated into this database, all of these results being reported recently. These advances continue to increase the utility of Ciona intestinalis as a model organism whilst the integrated database will be useful for researchers in comparative and evolutionary genomics.

Animals↗

Methods and pitfalls in searching drug safety databases utilising the Medical Dictionary for Regulatory Activities (MedDRA).

The Medical Dictionary for Regulatory Activities (MedDRA) is a unified standard terminology for recording and reporting adverse drug event data. Its introduction is widely seen as a significant improvement on the previous situation, where a multitude of terminologies of widely varying scope and quality were in use. However, there are some complexities that may cause difficulties, and these will form the focus for this paper. Two methods of searching MedDRA-coded databases are described: searching based on term selection from all of MedDRA and searching based on terms in the safety database. There are several potential traps for the unwary in safety searches. There may be multiple locations of relevant terms within a system organ class (SOC) and lack of recognition of appropriate group terms; the user may think that group terms are more inclusive than is the case. MedDRA may distribute terms relevant to one medical condition across several primary SOCs. If the database supports the MedDRA model, it is possible to perform multiaxial searching: while this may help find terms that might have been missed, it is still necessary to consider the entire contents of the SOCs to find all relevant terms and there are many instances of incomplete secondary linkages. It is important to adjust for multiaxiality if data are presented using primary and secondary locations. Other sources for errors in searching are non-intuitive placement and the selection of terms as preferred terms (PTs) that may not be widely recognised. Some MedDRA rules could also result in errors in data retrieval if the individual is unaware of these: in particular, the lack of multiaxial linkages for the Investigations SOC, Social circumstances SOC and Surgical and medical procedures SOC and the requirement that a PT may only be present under one High Level Term (HLT) and one High Level Group Term (HLGT) within any single SOC. Special Search Categories (collections of PTs assembled from various SOCs by searching all of MedDRA) are limited by the small number available and by lack of clarity about criteria applied in their construction. Difficulties in database searching may be addressed by suitable user training and experience, and by central reporting of detected deficiencies in MedDRA. Other remedies may include regulatory guidance on implementation and use of MedDRA. Further systematic review of MedDRA is needed and generation of standardised searches that may be used 'off the shelf' will help, particularly where the same search is performed repeatedly on multiple data sets. Until these enhancements are widely available, MedDRA users should take great care when searching a safety database to ensure that cases are not inadvertently missed.

Adverse Drug Reaction Reporting Systems↗

Ligand.Info small-molecule Meta-Database.

Ligand.Info is a compilation of various publicly available databases of small molecules. The total size of the Meta-Database is over 1 million entries. The compound records contain calculated three-dimensional coordinates and sometimes information about biological activity. Some molecules have information about FDA drug approving status or about anti-HIV activity. Meta-Database can be downloaded from the http://Ligand.Info web page. The database can also be screened using a Java-based tool. The tool can interactively cluster sets of molecules on the user side and automatically download similar molecules from the server. The application requires the Java Runtime Environment 1.4 or higher, which can be automatically downloaded from Sun Microsystems or Apple Computer and installed during the first use of Ligand.Info on desktop systems, which support Java (Ms Windows, Mac OS, Solaris, and Linux). The Ligand.Info Meta-Database can be used for virtual high-throughput screening of new potential drugs. Presented examples showed that using a known antiviral drug as query the system was able to find others antiviral drugs and inhibitors.

Databases, Genetic↗

Wireless access to a pharmaceutical database: a demonstrator for data driven Wireless Application Protocol (WAP) applications in medical information processing.

BACKGROUND: The Wireless Application Protocol technology implemented in newer mobile phones has built-in facilities for handling much of the information processing needed in clinical work. OBJECTIVES: To test a practical approach we ported a relational database of the Danish pharmaceutical catalogue to Wireless Application Protocol using open source freeware at all steps. METHODS: We used Apache 1.3 web software on a Linux server. Data containing the Danish pharmaceutical catalogue were imported from an ASCII file into a MySQL 3.22.32 database using a Practical Extraction and Report Language script for easy update of the database. Data were distributed in 35 interrelated tables. Each pharmaceutical brand name was given its own card with links to general information about the drug, active substances, contraindications etc. Access was available through 1) browsing therapeutic groups and 2) searching for a brand name. The database interface was programmed in the server-side scripting language PHP3. RESULTS: A free, open source Wireless Application Protocol gateway to a pharmaceutical catalogue was established to allow dial-in access independent of commercial Wireless Application Protocol service providers. The application was tested on the Nokia 7110 and Ericsson R320s cellular phones. CONCLUSIONS: We have demonstrated that Wireless Application Protocol-based access to a dynamic clinical database can be established using open source freeware. The project opens perspectives for a further integration of Wireless Application Protocol phone functions in clinical information processing: Global System for Mobile communication telephony for bilateral communication, asynchronous unilateral communication via e-mail and Short Message Service, built-in calculator, calendar, personal organizer, phone number catalogue and Dictaphone function via answering machine technology. An independent Wireless Application Protocol gateway may be placed within hospital firewalls, which may be an advantage with respect to security. However, if Wireless Application Protocol phones are to become effective tools for physicians, special attention must be paid to the limitations of the devices. Input tools of Wireless Application Protocol phones should be improved, for instance by increased use of speech control.

Clinical Pharmacy Information Systems↗

Just-in-time database-driven Web applications.

"Just-in-time" database-driven Web applications are inexpensive, quickly-developed software that can be put to many uses within a health care organization. Database-driven Web applications garnered 73873 hits on our system-wide intranet in 2002. They enabled collaboration and communication via user-friendly Web browser-based interfaces for both mission-critical and patient-care-critical functions. Nineteen database-driven Web applications were developed. The application categories that comprised 80% of the hits were results reporting (27%), graduate medical education (26%), research (20%), and bed availability (8%). The mean number of hits per application was 3888 (SD = 5598; range, 14-19879). A model is described for just-in-time database-driven Web application development and an example given with a popular HTML editor and database program.

Database Management Systems↗

Development of a digital image database for chest radiographs with and without a lung nodule: receiver operating characteristic analysis of radiologists' detection of pulmonary nodules.

OBJECTIVE: We developed a digital image database (www.macnet.or.jp/jsrt2/cdrom_nodules.html ) of 247 chest radiographs with and without a lung nodule. The aim of this study was to investigate the characteristics of image databases for potential use in various digital image research projects. Radiologists' detection of solitary pulmonary nodules included in the database was evaluated using a receiver operating characteristic (ROC) analysis. MATERIALS AND METHODS: One hundred and fifty-four conventional chest radiographs with a lung nodule and 93 radiographs without a nodule were selected from 14 medical centers and were digitized by a laser digitizer with a 2048 x 2048 matrix size (0.175-mm pixels) and a 12-bit gray scale. Lung nodule images were classified into five groups according to the degrees of subtlety shown. The observations of 20 participating radiologists were subjected to ROC analysis for detecting solitary pulmonary nodules. Experimental results (areas under the curve, Az) obtained from observer studies were used for characterization of five groups of lung nodules with different degrees of subtlety. RESULTS: ROC analysis showed that the database included a wide range of various nodules yielding Az values from 0.574 to 0.991 for the five categories of cases for different degrees of subtlety. CONCLUSION: This database can be useful for many purposes, including research, education, quality assurance, and other demonstrations.

Adult↗

HBVPathDB: a database of HBV infection-related molecular interaction network.

AIM: To describe molecules or genes interaction between hepatitis B viruses (HBV) and host, for understanding how virus' and host's genes and molecules are networked to form a biological system and for perceiving mechanism of HBV infection. METHODS: The knowledge of HBV infection-related reactions was organized into various kinds of pathways with carefully drawn graphs in HBVPathDB. Pathway information is stored with relational database management system (DBMS), which is currently the most efficient way to manage large amounts of data and query is implemented with powerful Structured Query Language (SQL). The search engine is written using Personal Home Page (PHP) with SQL embedded and web retrieval interface is developed for searching with Hypertext Markup Language (HTML). RESULTS: We present the first version of HBVPathDB, which is a HBV infection-related molecular interaction network database composed of 306 pathways with 1 050 molecules involved. With carefully drawn graphs, pathway information stored in HBVPathDB can be browsed in an intuitive way. We develop an easy-to-use interface for flexible accesses to the details of database. Convenient software is implemented to query and browse the pathway information of HBVPathDB. Four search page layout options-category search, gene search, description search, unitized search-are supported by the search engine of the database. The database is freely available at http://www.bio-inf.net/HBVPathDB/HBV/. CONCLUSION: The conventional perspective HBVPathDB have already contained a considerable amount of pathway information with HBV infection related, which is suitable for in-depth analysis of molecular interaction network of virus and host. HBVPathDB integrates pathway data-sets with convenient software for query, browsing, visualization, that provides users more opportunity to identify regulatory key molecules as potential drug targets and to explore the possible mechanism of HBV infection based on gene expression datasets.

Databases, Genetic↗

Off-label use of proton pump inhibitors and P-blockers in general practices: an analysis using the Disease Analyzer--mediplus patient database.

OBJECTIVE: The off-label use of medicines is a widespread phenomenon in medical practice but discussion on the legality of using drugs outside their licensed indications is still ongoing. Prescription recommendations and prescribing habits can differ greatly. We have used a database tool to analyze replies to a batch of questions which included the question "Is the off-label use of medications common?". The analysis was carried out using the Disease Analyzer--mediplus patient database, which is a database tool registered in Germany. It enabled the anonymous access to a representative panel of physicians and patients. More than 1,500 medical practices representing approximately 2.5 million patients were analyzed in a cross-sectional or longitudinal manner. The Disease Analyzer--mediplus database is unique in that it has direct links to individual diagnoses and the corresponding therapy. RESULTS: The findings demonstrated that proton pump inhibitors (PPI), which are licensed for the treatment of gastric ulcer and gastric reflux, are also used off-label in gastritis. The off-label use varies from 30 - 40% of prescriptions. The data indicate that the prescribing behavior has been influenced by the ending of the patent protection on omeprazole. A second instance which has been identified involves the beta-blocker carvedilol, which is licensed for the treatment of heart failure (24% of the total number of patients receiving the drug) but it was found that other beta-blockers are used off-label in this indication at a rate of more than 10% of prescriptions. CONCLUSION: The off-label use of drugs is high, especially in gastritis and heart failure. The investigation has also confirmed that the Disease Analyzer--mediplus database provides quantitative and qualitative analyses combining all relevant information concerning physicians, patients, diagnoses and therapy and that this information can be used to evaluate prescribing habits and trends with regard to the off-label use of drugs.

Adolescent↗

Databases in the next millennium.

Predicting the likelihood that large databases will become an important instrument for medical quality improvement is at least as difficult as most prognostication. This attempt at prediction starts by trying to ask the right questions: Can data serve as the agent for meaningful improvement? Is meaningful improvement possible without data? What elements are necessary and sufficient for improving the quality of medical care? It then looks for answers, starting with an unconventional excursion into the history of database use. This is followed by a recognition that the use of large databases for medical quality improvement is a true innovation, the future of which will probably be determined as much by the social and emotional forces that govern the diffusion of all innovations as by the technical strength of databases themselves. Finally, it examines some of the limitations and pitfalls that are likely to be associated with the increasing use of large databases in medicine.

Databases, Factual↗

The Wenger Eskimo Anthropological Database: a valuable research tool.

The goal of the Wenger Eskimo Database Project is to develop a full-text database of early and primary written ethnographic sources in English on Inuit/Eskimo peoples and to make it available on CD-ROM, both to northern residents and to students and researchers dealing with northern topics. This paper describes the database, sets out a brief history of its growth, and describes recent developments, including the addition of new materials and a Windows format. The paper includes a demonstration of how the database may be used for health-related research. The database is available free of charge to nonprofit institutions that are willing to meet some simple, basic requirements.

Alaska↗