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PubMed2007

Protein identification by tandem mass spectrometry and sequence database searching.

The shotgun proteomics strategy, based on digesting proteins into peptides and sequencing them using tandem mass spectrometry (MS/MS), has become widely adopted. The identification of peptides from acquired MS/MS spectra is most often performed using the database search approach. We provide a detailed description of the peptide identification process and review the most commonly used database search programs. The appropriate choice of the search parameters and the sequence database are important for successful application of this method, and we provide general guidelines for carrying out efficient analysis of MS/MS data. We also discuss various reasons why database search tools fail to assign the correct sequence to many MS/MS spectra, and draw attention to the problem of false-positive identifications that can significantly diminish the value of published data. To assist in the evaluation of peptide assignments to MS/MS spectra, we review the scoring schemes implemented in most frequently used database search tools. We also describe statistical approaches and computational tools for validating peptide assignments to MS/MS spectra, including the concept of expectation values, reversed database searching, and the empirical Bayesian analysis of PeptideProphet. Finally, the process of inferring the identities of the sample proteins given the list of peptide identifications is outlined, and the limitations of shotgun proteomics with regard to discrimination between protein isoforms are discussed.

Amino Acid Sequence↗
PubMed2005

Construction and validation of a population-based bone densitometry database.

Utilization of dual-energy X-ray absorptiometry (DXA) for the initial diagnostic assessment of osteoporosis and in monitoring treatment has risen dramatically in recent years. Population-based studies of the impact of DXA and osteoporosis remain challenging because of incomplete and fragmented test data that exist in most regions. Our aim was to create and assess completeness of a database of all clinical DXA services and test results for the province of Manitoba, Canada and to present descriptive data resulting from testing. A regionally based bone density program for the province of Manitoba, Canada was established in 1997. Subsequent DXA services were prospectively captured in a program database. This database was retrospectively populated with earlier DXA results dating back to 1990 (the year that the first DXA scanner was installed) by integrating multiple data sources. A random chart audit was performed to assess completeness and accuracy of this dataset. For comparison, testing rates determined from the DXA database were compared with physician administrative claims data. There was a high level of completeness of this database (>99%) and accurate personal identifier information sufficient for linkage with other health care administrative data (>99%). This contrasted with physician billing data that were found to be markedly incomplete. Descriptive data provide a profile of individuals receiving DXA and their test results. In conclusion, the Manitoba bone density database has great potential as a resource for clinical and health policy research because it is population based with a high level of completeness and accuracy.

Absorptiometry, Photon↗
PubMed2003

Text mining neuroscience journal articles to populate neuroscience databases.

We have developed a program NeuroText to populate the neuroscience databases in SenseLab (http://senselab.med.yale.edu/senselab) by mining the natural language text of neuroscience articles. NeuroText uses a two-step approach to identify relevant articles. The first step (pre-processing), aimed at 100% sensitivity, identifies abstracts containing database keywords. In the second step, potentially relevant abstracts identified in the first step are processed for specificity dictated by database architecture, and neuroscience, lexical and semantic contexts. NeuroText results were presented to the experts for validation using a dynamically generated interface that also allows expert-validated articles to be automatically deposited into the databases. Of the test set of 912 articles, 735 were rejected at the pre-processing step. For the remaining articles, the accuracy of predicting database-relevant articles was 85%. Twenty-two articles were erroneously identified. NeuroText deferred decisions on 29 articles to the expert. A comparison of NeuroText results versus the experts' analyses revealed that the program failed to correctly identify articles' relevance due to concepts that did not yet exist in the knowledgebase or due to vaguely presented information in the abstracts. NeuroText uses two "evolution" techniques (supervised and unsupervised) that play an important role in the continual improvement of the retrieval results. Software that uses the NeuroText approach can facilitate the creation of curated, special-interest, bibliography databases.

Abstracting and Indexing↗
PubMed2004

Update of mouse microsatellite database of Japan (MMDBJ).

We updated a database of microsatellite marker polymorphisms found in inbred strains of the mouse, most of which were derived from the wild stocks of four Mus musculus subspecies, M. m. domesticus, M. m. musculus, M. m.castaneus and M. m. molossinus. The major aim of constructing this database was to establish the genetic status of these inbred strains as resources for linkage analysis and positional cloning. The inbred strains incorporated in our database are A/J, C57BL/6J, CBA/J, DBA/2J, SM/J, SWR/J, 129Sv/J, MSM/Ms, JF1/Ms, CAST/Ei, NC/Nga, BLG2/Ms, NJL/Ms, PGN2/Ms, SK/CamEi and SWN/Ms, which have not or have only been poorly incorporated in the Whitehead Institute/MIT (WI/MIT) microsatellite database. The number of polymorphic microsatellite loci incorporated in our database is over 1,000 in all strains, and the URL site for our database is located at http:// www.shigen.nig.ac.jp /mouse/mmdbj/mouse.html.

Animals↗
PubMedDate not supplied

The development and validation of a geographic information system database for the poultry industry on the Delmarva Peninsula.

A geographic information system (GIS) database of the poultry industry on the Delmarva Peninsula was developed through a cooperative agreement between the Delmarva Poultry Industry, Inc., and the Virginia-Maryland Regional College of Veterinary Medicine. The purpose of this database was to facilitate disease surveillance and assist in managing the response to outbreaks and other emergencies. Two methods of data collection were employed and are described in this paper. The first method was to visit each poultry farm and collect the latitude and longitude coordinates with a handheld global positioning system unit. The second method used property ownership information, aerial photographs, and a GIS to determine the latitude and longitude of each poultry farm. There was no significant difference between the two methods in the accuracy of the results, but there was a large difference in the amount of time and money necessary to obtain the data. These findings indicate that whereas there are many ways to obtain accurate data for a GIS database, other factors may influence which method is chosen. A subset of farms contained within the database was visited to assess the accuracy of the locations contained within the database. Of the 240 farms visited for validation, 212 showed evidence of a functioning or previously functioning poultry operation. The corresponding error rate was 11%. This demonstrates the need to assure that the database is kept up to date to ensure that attrition among poultry growers is recorded. Several potential factors that might contribute to sources of error are discussed.

Agriculture↗
PubMed2006

Bias due to false-positive diagnoses in an automated health insurance claims database.

BACKGROUND AND OBJECTIVE: Automated database studies have become a cornerstone of drug safety assessment. To assess the reliability of automated data, we compared the hospitalisation and mortality rates among three similar studies of automated healthcare databases in North America. METHODS: Similar protocols were used to identify patients diagnosed with chronic obstructive pulmonary disease (COPD) who were treated with inhaled bronchodilators or inhaled corticosteroids in the Saskatchewan Health Database (SHD), the Kaiser Permanente Medical Care Program (KPMCP) of Northern California, and a proprietary automated insurance claims database available from i3 (formerly Ingenix). Automated data were used to compute incidence rates of total hospitalisation, cardiovascular (CV) hospitalisation and hospitalisation due to several specific types of CV outcomes. Record linkage with registries of vital statistics was used to identify deaths, obtain death certificates, and compute rates of total mortality, CV mortality and deaths due to certain CV outcomes. We compared rates in the i3 population with rates in the other two populations using age-adjusted rate ratio estimates and 95% CIs. RESULTS: The i3 cohort had approximately one-half the rates of total mortality, CV mortality and total hospitalisations, but twice the rate of CV hospitalisations, compared with each of the other two database cohorts. DISCUSSION: The unexpectedly higher rates of CV hospitalisations in the i3 population are inconsistent with its lower CV mortality, total mortality and total hospitalisation rates. This discrepancy is not readily explained by a higher prevalence of CV disease or procedures, random variation or confounding. Instead, high CV hospitalisation rates in the i3 population are consistent with a high rate of false-positive diagnoses recorded on insurance billing claims. CONCLUSION: These results underscore the importance of ensuring valid endpoints in automated claims databases.

Bias↗
PubMed2004

Assessing the use of retrospective databases in conducting economic evaluations of drugs: the case of asthma.

When evaluating drug substances, the traditional clinical study setting does not allow scope for observing real-life behaviour since all alternative actions are determined beforehand. However, a study based on prospective or retrospective databases containing real-life data can examine how patients and physicians behave in a real-world setting and can investigate the relationship between the introduction of a drug and the amount of healthcare used in actual practice. We reviewed the quality and potential policy application of published retrospective database studies in which an economic evaluation of the use of drugs in asthma was conducted. A search in literature databases found 16 such studies, which were reviewed and evaluated according to a published checklist. No article fulfilled all the criteria for a 'good' economic evaluation. The results of many of the evaluations may be informative, but not transparent enough to deliver policy conclusions. This may limit the use of the currently published retrospective database studies as a base for policy decision, compared with randomised controlled trials, despite the additional value of these database analyses when well conducted. A greater transparency when presenting material and results is therefore called for, to increase the usefulness of database studies.

Anti-Asthmatic Agents↗
PubMed2005

The diffusion of health economics knowledge in Europe : The EURONHEED (European Network of Health Economics Evaluation Database) project.

This paper overviews the EURONHEED (EUROpean Network of Health Economics Evaluation Databases) project. Launched in 2003, this project is funded by the EU. Its aim is to create a network of national and international databases dedicated to health economic evaluation of health services and innovations. Seven centres (France, Germany, Italy, The Netherlands, Spain, Sweden and the UK) are involved covering 17 countries. The network is based on two existing databases, the French CODECS (COnnaissance et Decision en EConomie de la Sante) database, created in 2000 by the French Health Economists Association (College des Economistes de la Sante), and the UK NHS-EED (NHS Economic Electronic Database), run by the Centre for Reviews and Dissemination, University of York, York, England. The network will provide bibliographic records of published full health economic evaluation studies (cost-benefit, cost-utility and cost-effectiveness studies) as well as cost studies, methodological articles and review papers. Moreover, a structured abstract of full evaluation studies will be provided to users, allowing them access to a detailed description of each study and to a commentary stressing the implications and limits, for decision making, of the study. Access will be free of charge. The database features and its ease of access (via the internet: http://www.euronheed.org) should facilitate the diffusion of existing economic evidence on health services and the generalisation of common standards in the field at the European level, thereby improving the quality, generalisability and transferability of results across countries.

Databases as Topic↗
PubMed1994

Neuropsychiatric adverse drug reactions: passive reports to Health and Welfare Canada's adverse drug reaction database (1965-present).

OBJECTIVE: Since 1965, Health and Welfare Canada has operated an adverse drug reaction (ADR) program. The program accepts spontaneous reports of adverse drug reactions, and maintains an ADR database. The purpose of this article is to summarize the Psychiatric ADRs reported to this database since 1965. The nature of the information prohibits its use in the evaluation of epidemiological hypotheses about the etiology of drug-induced mental disorders. However, in an exploratory sense, the contents of the database may contribute to the development of epidemiological hypotheses about the etiology of drug-induced mental disorders. Of particular interest are areas of apparent contradiction between the contents of the database and the clinical literature. METHODS: The database was searched for reports of ADRs to a group of drugs which have been frequently implicated in causing psychiatric toxicity. All reports characterized as "psychiatric disorders" were down-loaded from the database for the analysis (n = 1822). The reports were further classified into nine categories according to the type of psychiatric symptoms described. RESULTS: There were several reports of hallucinations caused by methyldopa, and also several reports of benzodiazepine-induced hallucinations and encephalopathy. These reactions have not been described in the literature. Also, there were few reports of digoxin-induced organic depression, and an absence of reports of organic mania induced by H-2 blockers, despite descriptions of these sorts of reactions in the clinical literature. CONCLUSIONS: Further research is needed to define the neuropsychiatric toxicity associated with medical drugs. Clinicians must continue to consider the potential role of medications in the etiology of psychiatric symptoms.

Adverse Drug Reaction Reporting Systems↗
PubMedDate not supplied

Design of hospital database systems in a non-relational environment.

The lack of an appropriate, widely accepted, design procedure for use with non-relational database management systems has been a major, common problem in many efforts to develop an integrated hospital database. The availability of such a design procedure is particularly important today since the majority of the database management systems currently in use are non-relational. A database design procedure is proposed which should assist with the design of optimal non-relational hospital database systems. The proposed design procedure is separated into two distinct steps: the development of an appropriate intermediate relational database structure and the subsequent development of an equivalent non-relational one. A set of rules is given for the move from the proposed intermediate relational to the equivalent non-relational structure. An example application from the hospital environment is also included in order to better demonstrate the process.

Computer Communication Networks↗
PubMedDate not supplied

Review of the studies cited in the DataBase section of the American Journal of Health Promotion.

PURPOSE OF THE REVIEW: To analyze the characteristics of the articles reviewed in the DataBase section of the American Journal of Health Promotion and to summarize this review in tabular format. DATA SOURCES: All 350 entries in the American Journal of Health Promotion DataBase section beginning with issue 1:3 (Winter 1987) through issue 17:3 (January/February 2003) were included in this review. STUDY INCLUSION AND EXCLUSION CRITERIA: Every study summarized in the DataBase section was included. Five duplicate sets of entries existed in the DataBase section. One entry from each set was excluded based upon author consensus. Thus, this review includes 345 unique entries. DATA EXTRACTION METHODS: All data reported in the DataBase section (e.g., sample sizes, measurement tools, study duration), as well as additional data derived directly from the studies (i.e., cross-sectional versus longitudinal study design, unit of analysis, and study topic) were entered in SPSS 11.5 for PC (SPSS, Inc, Chicago, Illinois). DATA SYNTHESIS: Data were synthesized to identify the frequency of entry by research question, research design and internal validity rating, unit of analysis, measurement tool(s), and health topics addressed. MAJOR CONCLUSIONS: The majority of articles included in the DataBase received the highest research design rating, had robust sample sizes, and were of a meaningful duration. Additionally, a wide variety of topics were addressed. Overall, these strengths indicate that a solid foundation of research has been established on many of the most critical issues facing the health promotion field.

Behavioral Research↗
PubMed2002

Use of the mediplus patient database in healthcare research.

OBJECTIVE: Public health systems require fast and precise analyses of physicians' day-to-day diagnoses and therapy behavior regarding qualitative, safety or economical aspects. A partnership between physicians in practices and a database organization (IMS Health, Frankfurt, Germany) which has been in existence for more than 10 years has developed a procedure for documenting various types of studies with regard to diagnosis and therapy behavior. This endeavor has facilitated scientific progress by providing precise analytical information and guidelines. METHODS: The database used has the name mediplus. It is a longitudinal patient database with anonymous access to a representative and valid panel of physicians and patients in Germany. A total of more than 1,000 medical practices and over 75 million prescriptions have been documented in a cross and/or longitudinal section. The longest time period per patient is more than 10 years starting in 1989, with monthly updates. RESULTS: Analyses have been obtained detailing prescription behavior of doctors regarding diabetes therapy and enable recommendations to be made regarding the therapy of migraine and the eradication of Helicobacter pylori infections. Information is also retrievable on drug safety studies in general and the extent to which hospitals influence the prescription behavior of doctors treating patients after discharge. DISCUSSION: The mediplus patient database combines all decision relevant information on physicians, patients, diagnoses and course of therapies and thus makes possible the investigation of the courses of diseases and therapy patterns. The monthly update enables trends to be identified at an early stage. The mediplus database is an ideal instrument for the enforcement of quantitative and qualitative analyses of patient histories because it directly links the individual diagnoses with the corresponding therapies. The database is currently undergoing extension with additional specialist groups such as pediatricians, neurologists, orthopedists, urologists, ENT specialists, surgeons and pulmonologists.

Databases, Factual↗
PubMed1997

Internet image database: development and implementation.

The widespread acceptance of World Wide Web (WWW) hypermedia protocols allows rapid cross-platform development of database interfaces. Using the WWW as the interface promotes easy integration of databases with other publicly available Internet resources. We present our experience with an image database search program (IDBS) developed on the PC platform using freely available UNIX development tools. The database routines were written in PERL. The image database program provides a familiar user interface to a collection of clinical images stored in digital form, either on local media or on the Internet. The design goals of the project and the strategies used to meet them are presented. The source code and a demonstration database are available on the Internet at http:/(/)www.webmedix.com/idbs.

Computer Communication Networks↗
PubMed1998

Prevalence and cost of hospitalization for gastrointestinal complications related to peptic ulcers with bleeding or perforation: comparison of two national databases.

The purpose of this study was to determine the prevalence and cost of hospitalization for upper gastrointestinal complications, including peptic ulcers with hemorrhage or perforation. Upper gastrointestinal complications and corresponding economic data were obtained from two sources. The first was a 20% sample of all community hospital discharges (about 6 million per year) from 11 states for 1991 and 1992 Hospital Cost Utilization Project; HCUP-3). The second source of data was a claims database for employees of large US corporations and their dependents for 1992, 1993, and 1994 (about 3.5 million covered lives per year; MarketScan). A group of ICD-9 codes for the diagnosis of peptic and gastroduodenal ulcers with bleeding or perforation were used to identify hospital admissions because of upper gastrointestinal complications. Similar patterns were observed across the MarketScan and HCUP-3 databases regarding hospitalization with diagnoses related to gastrointestinal complications identified according to the ICD-9 codes. The average age of patients with upper gastrointestinal complications was 66 years in the HCUP-3 database and 52 years in the MarketScan database. The average annual rates of upper gastrointestinal complications as a primary or secondary diagnosis were 6.4 and 6.7 per 1000 discharges for 1991 and 1992, respectively (HCUP-3), and 4.3, 4.2, and 4.9 per 1000 admissions for 1992, 1993, and 1994, respectively (MarketScan). The average length of stay for upper gastrointestinal complications as a primary diagnosis was 7.8 days in 1991 and 7.5 days in 1992 (HCUP-3) and 6.1, 5.1, and 5.1 days in 1992, 1993, and 1994, respectively (MarketScan). The national average total charge for hospitalization for gastrointestinal problems as a primary diagnosis was $12,970 in 1991 and $14,294 in 1992 (HCUP-3). The average total reimbursement for hospitalizations related to upper gastrointestinal problems was $15,309 in 1992, $12,987 in 1993, and $13,150 in 1994 (MarketScan). Hospital admissions for upper gastrointestinal complications are expensive. The rate and cost per admission are higher for the older population. The results on the elements covered by both databases are consistent. Therefore the databases complement each other on the type of information abstracted.

Cost of Illness↗
PubMed1998

IMGT, the international ImMunoGeneTics database: a new design for immunogenetics data access.

IMGT, the international ImMunoGeneTics database is an integrated database specializing in Immunoglobulins (Ig), T-cell receptors (TcR) and MHC molecules of all vertebrate species, created by Marie-Paule Lefranc, University of Montpellier, CNRS, Montpellier, France (Nucleic Acids Research, Database issue, Vol 26, January 1998). IMGT includes three databases: LIGM-DB (for Ig and TcR), MHC/HLA-DB and IMGT/PRIMER-DB (an Ig, TcR and MHC-related primer database), the last two in development. IMGT comprises expertly annotated sequences and alignment tables. LIGM-DB contains more than 24.000 Immunoglobulin and T cell Receptor sequences from 81 different species. MHC/HLA-DB contains class I and class II Human Leucocyte Antigen alignment tables. An IMGT tool, DNAPLOT, developed for Ig, TcR and MHC sequence analysis, is also available. IMGT goals are to establish a common data access to all immunogenetics data, including nucleotide and protein sequences, oligonucleotide primers, gene maps and other genetic data of Ig, TcR and MHC molecules, from all species, and to provide a graphical user friendly data access. IMGT has important implications in medical research (repertoire in autoimmune diseases, AIDS, leukemias, lymphomas), therapeutical approaches (antibody engineering), genome diversity and genome evolution studies. In this paper, we describe our approach for the data modelisation, the automation of the annotation procedure and control of data quality in LIGM-DB database. IMGT is freely available on the CNUSC WWW server at Montpellier: http://imgt.cnusc.fr: 8104 (contact: Denys.Chaume@cnusc.fr) and on the EBI servers: http://www.ebi.ac.uk/imgt (contact: malik@ebi.ac.uk) and ftp.ebi.ac.uk/pub/databases/imgt. LIGM-DB users are encouraged to report errors or suggestions to giudi@ligm.crbm.cnrs-mop.fr. IMGT initiator and coordinator: Marie-Paule Lefranc, lefranc@ligm.crbm.cnrs-mop.fr. (fax: +33(0)467040231).

Amino Acid Sequence↗
PubMed1999

Quality-assessed reviews of health care interventions and the database of abstracts of reviews of effectiveness (DARE). NHS CRD Review, Dissemination, and Information Teams.

OBJECTIVES: Database of Abstracts of Reviews of Effectiveness (DARE) (http:@www.york.ac.uk/inst/crd/) at the NHS Centre for Reviews and Dissemination provides a unique international resource of structured summaries of quality-assessed reviews of health care interventions. These reviews have been identified from searches of electronic databases and by hand-searching journals. This paper describes and summarizes the DARE database, including the topic areas covered and the review methods used. METHODS: The first 480 structured abstracts on the DARE database were summarized. Data were extracted from each database field and coded for analysis. RESULTS: Most of the systematic reviews investigated the effectiveness of treatments: 54% investigated the effectiveness of medical therapies, and 10% assessed surgical interventions. Around two-thirds used meta-analytic methods to combine primary studies. The quality of the reviews was variable, with just over half of the reviews (52%, n = 251) having systematically assessed the validity of the included primary studies. Narrative reviews were more likely than meta-analyses to reach negative conclusions (42% vs. 25%, p = .0001). The 21 reviews that reported drug company funding were more likely to reach positive conclusions (81% vs. 66%, p = .15). CONCLUSION: The DARE database is a valuable source of quality-assessed systematic reviews, and is free and easily accessible. It provides a valuable online resource to help in filtering out poorer quality reviews when assessing the effectiveness of health technologies.

Abstracting and Indexing↗
PubMed1999

National health care providers' database (NHCPD) of Slovenia--information technology solution for health care planning and management.

INTRODUCTION: The article describes the possibilities of planning of the health care providers' network enabled by the use of information technology. The cornerstone of such planning is the development and establishment of a quality database on health care providers, health care professionals and their employment statuses. MATERIAL AND METHODS: Based on the analysis of information needs, a new database was developed for various users in health care delivery as well as for those in health insurance. The method of information engineering was used in the standard four steps of the information system construction, while the whole project was run in accordance with the principles of two internationally approved project management methods. Special attention was dedicated to a careful analysis of the users' requirements and we believe the latter to be fulfilled to a very large degree. RESULTS: The new NHCPD is a relational database which is set up in two important state institutions, the National Institute of Public Health and the Health Insurance Institute of Slovenia. The former is responsible for updating the database, while the latter is responsible for the technological side as well as for the implementation of data security and protection. NHCPD will be inter linked with several other existing applications in the area of health care, public health and health insurance. Several important state institutions and professional chambers are users of the database in question, thus integrating various aspects of the health care system in Slovenia. CONCLUSIONS: The setting up of a completely revised health care providers' database in Slovenia is an important step in the development of a uniform and integrated information system that would support top decision-making processes at the national level.

Databases, Factual↗
PubMed2000

Creating local bibliographic databases: new tools for evidence-based health care.

The Internet has created new opportunities for librarians to present literature search results to clinicians. In order to take full advantage of these opportunities, libraries need to create locally maintained bibliographic databases. A simple method of creating a local bibliographic database and publishing it on the Web is described. The method uses off-the-shelf software and requires minimal programming. A hedge search strategy for outcome studies of clinical process interventions is created, and Ovid is used to search MEDLINE. The search results are saved and imported into EndNote libraries. The citations are modified, exported to a Microsoft Access database, and published on the Web. Clinicians can use a Web browser to search the database. The bibliographic database contains 13,803 MEDLINE citations of outcome studies. Most searches take between four and ten seconds and retrieve between ten and 100 citations. The entire cost of the software is under $900. Locally maintained bibliographic databases can be created easily and inexpensively. They significantly extend the evidence-based health care services that libraries can offer to clinicians.

Costs and Cost Analysis↗