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PubMed1993

Validity of rheumatoid arthritis diagnoses listed in the Saskatchewan Hospital Separations Database.

A Saskatchewan hospital separations database was compared to abstracted hospital records to determine the reliability of the database (i.e. accuracy with which the computer data reflect the charts from which they were coded) and the validity of classifying rheumatoid arthritis status with the database (i.e. the extent to which rheumatoid arthritis mentioned in the database reflected the condition of the patient). A sample of hospitalized subjects fell into three categories: 144 who never had a database diagnosis of any arthritis, 146 who had a database diagnosis of osteoarthritis, and 142 who had a database diagnosis of rheumatoid arthritis. These 432 people experienced 1717 hospitalizations eligible to match a hospital database listing by date, and 1618 matched. Of the remaining 99, 35 were relatively recent and probably had not yet been entered into the database, 39 were possibly entered incorrectly, and 25 could not be matched in any way. Of 150 hospitalizations with a database diagnosis of rheumatoid arthritis, this diagnosis was in the hospital record for 125. Chart documentation of rheumatoid arthritis status was greatest for subjects who, according to the database, were hospitalized by a rheumatologist: of 73 subjects in this category, abstractions showed 69.9% met > or = 5 American Rheumatism Association criteria, 15.1% met < 5 criteria but had a rheumatologist's diagnosis of rheumatoid arthritis, 1.3% met < 5 criteria and had a rheumatoid arthritis diagnosis by a non-rheumatologist, and 13.7% had no mention of rheumatoid arthritis or its symptoms in any medical record abstracted. In summary, reliability of the database was excellent, but validity depended on the source of diagnosis.

Arthritis, Rheumatoid↗

PubMed1999

Can cardiovascular clinical characteristics be identified and outcome models be developed from an in-patient claims database?

The objective of this study was to assess whether administrative (claims) databases can be used to assess clinical variables and predict outcome. Although administrative databases are useful for assessing resource utilization, their utility for assessing clinical information is less certain. Prospectively gathered clinical databases, however, are expensive and not widely available. The UB92 formulation of the hospital bill was used as an administrative source of data and compared with the clinical cardiovascular database at Emory University. The claims database was compared with the clinical database for 11 variables. Outcome models were developed with multivariate methods. A total of 11,883 patients who underwent catheterization (5,255 underwent percutaneous transluminal coronary angioplasty [PTCA] and 3,794 underwent coronary artery bypass surgery [CABG]) between 1991 and 1995 were included. For some variables, the claims database correlated well (diabetes, sensitivity 87%, specificity 99%), whereas for others the claims database was less accurate (peripheral vascular disease, sensitivity 20%, specificity 99%). Uncertain coding in the claims database, which can result in the same code being used for co-morbid states and severity of disease, as well as complications, limited the ability of claims to predict outcome. Clinical databases may also be limited by lack of objectivity and missing data. The utility of claims databases to assess severity of disease and co-morbid states is limited, and outcome modeling and risk assessment from claims databases may be inappropriate and spurious. Developing better data standards and less expensive methods for acquisition of clinical data is necessary for improved outcome assessment.

Cardiovascular Diseases↗

PubMed1998

Assessment of bibliographic databases performance in information retrieval for occupational and environmental toxicology.

OBJECTIVE: To determine the efficiency of the major bibliographic databases by assessing the percentage of references among the total literature available that can be retrieved from each database. We also evaluated the best database combinations to carry out an exhaustive search. METHODS: BIOSIS, EMBASE, MEDLINE, NIOSH-TIC, and TOXLINE were searched on two topics: allergy to latex and asbestos and mesothelioma, in the title, abstract, or keywords (textwords). This search was performed for the years 1994 and 1995. All the records were classified by journal and author's name and were verified for each record whether or not it was indexed in each database. Statistical analysis was performed with chi 2 test. RESULTS: 777 articles in 510 issues were found. The efficiency of each database (percentage of articles recovered) and of combinations varied between 11% and 63% for one database and between 42% and 86% for a combination of two databases. The reasons why these differences exist between databases, and within a database, between two different subjects or two different years are reported. CONCLUSION: Firstly, it is not advisable to assert that a bibliography is complete when only one database is searched. Secondly, the efficiency of the databases may be quite different. Finally, it is suggested that the best way to be as exhaustive as possible is to search two or more databases-for example, in EMBASE and TOXLINE, or to a lesser extent EMBASE and MEDLINE. This seems to be the best compromise solution between time consumed for searching and efficiency.

Asbestos↗

PubMed1994

SORTEZ: a relational translator for NCBI's ASN.1 database.

The National Center for Biotechnology Information (NCBI) has created a database collection that includes several protein and nucleic acid sequence databases, a biosequence-specific subset of MEDLINE, as well as value-added information such as links between similar sequences. Information in the NCBI database is modeled in Abstract Syntax Notation 1 (ASN.1) an Open Systems Interconnection protocol designed for the purpose of exchanging structured data between software applications rather than as a data model for database systems. While the NCBI database is distributed with an easy-to-use information retrieval system, ENTREZ, the ASN.1 data model currently lacks an ad hoc query language for general-purpose data access. For that reason, we have developed a software package, SORTEZ, that transforms the ASN.1 database (or other databases with nested data structures) to a relational data model and subsequently to a relational database management system (Sybase) where information can be accessed through the relational query language, SQL. Because the need to transform data from one data model and schema to another arises naturally in several important contexts, including efficient execution of specific applications, access to multiple databases and adaptation to database evolution this work also serves as a practical study of the issues involved in the various stages of database transformation. We show that transformation from the ASN.1 data model to a relational data model can be largely automated, but that schema transformation and data conversion require considerable domain expertise and would greatly benefit from additional support tools.

Algorithms↗

PubMed1992

Human HPRT mutant database: software for data entry and retrieval.

We have developed a computer database containing information on over 1,000 human hypoxanthine guanine phosphoribosyl transferase (HPRT) mutants. Both published and unpublished data are present. The database itself is maintained in a dBASE format (.DBF) and we provide a set of programs to examine and extract information from the database. A program to input information into the database is also supplied. The database and programs are available directly from us or via remote FTP (file transfer protocol) using BITNET/INTERNET. All programs require an IBM-compatible computer, the MS-DOS operating system (version 3.3 or greater), and a hard disk with about 5 megabytes of free disk space. The purpose of the database is 1) to allow investigators to contribute their HPRT mutants directly to the database in a standardized fashion, and 2) to allow access to the entire database with a set of programs that allows manipulation and extraction of data. For example, using our programs it is possible to i) order the database by base pair position, ii) examine only information regarding mutagenesis by a particular agent, iii) search for a particular author, iv) create a report which contains selected portions of the database, the report can be printed or saved as a file. The database will be updated every several months and distributed.

Databases, Bibliographic↗

PubMed1996

An inequality for 3D database searching and its use in evaluating the treatment of conformational flexibility.

A mathematical formula is introduced for predicting the number of hits that should be observed in a flexible 3D database search, based on the results of a set of related queries. The projected number of hits is always greater than or equal to the actual number of hits, the discrepancy being due to imperfect treatment of conformational flexibility of the molecules. Hence, the difference between the projected and actual number of hits, delta, serves to measure how well conformational flexibility is being treated, in a manner that is objective, easy for a user to quickly verify, and independent of the particular algorithm for flexible 3D database search. It is shown that delta is a function both of how well conformational flexibility is treated and of the precision of the query. When the distance constraint is defined only to a precision of +/- 2.0 A, in a single-conformer database of drug-like molecules delta values of only 0.03 are found, while in a single-conformer database of di- and tripeptides, delta is 0.15. At increased precision, a flexible 3D database search becomes critical. For a single-conformer database, using a query of precision +/- 0.2 A, applied to a database of drug-like molecules, delta is 0.97; applied to a database of di- and tripeptides, delta is 2.21. By contrast, treating conformational flexibility by storing up to 100 conformers per molecule, at this precision, applied to a database of drug-like molecules, delta is 0.002; applied to a database of di- and tripeptides, delta is 0.07. This inequality, and hence delta, is defined only for database queries containing a single distance constraint; how the inequality may generalize to higher-dimensional queries is still unclear.

Algorithms↗

PubMed2002

Social benefits of non-criminal genetic databases: missing persons and human remains identification.

A Missing Persons Genetic Identification Program (Phoenix Program) was implemented in Spain in order to try to identify cadavers and human remains that could not be identified using traditional forensic approaches; to our knowledge, this is the first database ever implemented and in function in the world. Two separate mitochondrial DNA (mtDNA) databases have been generated and comparisons can be made automatically to match identical or similar sequences contained in both databases. One database is called the Reference Database (RD), which contains mtDNA sequences from maternal relatives of missing persons that provide the samples voluntarily after informed consent. The other database is called the Questioned Database (QD) and is comprised of mtDNA data on unknown remains and cadavers that could not be unequivocally identified. The combined database is a civil database designed solely for human identification and because of the informed consent and voluntary donation of reference samples is different from other databases now used to solve criminal cases. It is timely and incumbent on other willing countries to begin an international collaboration so compatibility and full utility can be enjoyed with this kind of non-criminal database.

Cadaver↗

PubMedDate not supplied

Evaluation of consumer drug information databases.

OBJECTIVES: To evaluate prescription drug information contained in six consumer drug information databases available on CD-ROM, and to make health care professionals aware of the information provided, so that they may appropriately recommend these databases for use by their patients. DESIGN: Observational study of six consumer drug information databases: The Corner Drug Store, Home Medical Advisor, Mayo Clinic Family Pharmacist, Medical Drug Reference, Mosby's Medical Encyclopedia, and PharmAssist. SETTING: Not applicable. PATIENTS OR OTHER PARTICIPANTS: Not applicable. INTERVENTIONS: Information on 20 frequently prescribed drugs was evaluated in each database. The databases were ranked using a point-scale system based on primary and secondary assessment criteria. MAIN OUTCOME MEASURES: For the primary assessment, 20 categories of information based on those included in the 1998 edition of the USP DI Volume II, Advice for the Patient: Drug Information in Lay Language were evaluated for each of the 20 drugs, and each database could earn up to 400 points (for example, 1 point was awarded if the database mentioned a drug's mechanism of action). For the secondary assessment, the inclusion of 8 additional features that could enhance the utility of the databases was evaluated (for example, 1 point was awarded if the database contained a picture of the drug), and each database could earn up to 8 points. RESULTS: The results of the primary and secondary assessments, listed in order of highest to lowest number of points earned, are as follows: Primary assessment--Mayo Clinic Family Pharmacist (379), Medical Drug Reference (251), PharmAssist (176), Home Medical Advisor (113.5), The Corner Drug Store (98), and Mosby's Medical Encyclopedia (18.5); secondary assessment--The Mayo Clinic Family Pharmacist (8), The Corner Drug Store (5), Mosby's Medical Encyclopedia (5), Home Medical Advisor (4), Medical Drug Reference (4), and PharmAssist (3). CONCLUSION: The Mayo Clinic Family Pharmacist was the most accurate and complete source of prescription drug information based on the USP DI Volume II and would be an appropriate database for health care professionals to recommend to patients.

CD-I↗

PubMed2000

The quest to deduce protein function from sequence: the role of pattern databases.

In the wake of the numerous now-fruitful genome projects, we have witnessed a 'tsunami' of sequence data and with it the birth of the field of bioinformatics. Bioinformatics involves the application of information technology to the management and analysis of biological data. For many of us, this means that databases and their search tools have become an essential part of the research environment. However, the rate of sequence generation and the haphazard proliferation of databases have made it difficult to keep pace with developments, even for the cognoscenti. Moreover, increasing amounts of sequence information do not necessarily equate with an increase in knowledge, and in the panic to automate the route from raw data to biological insight, we may be generating and propagating innumerable errors in our precious databases. In the genome era upon us, researchers want rapid, easy-to-use, reliable tools for functional characterisation of newly determined sequences. For the pharmaceutical industry in particular, the Pandora's box of bioinformatics harbours an information-rich nugget, ripe with potential drug targets and possible new avenues for the development of therapeutic agents. This review outlines the current status of the major pattern databases now used routinely in the analysis of protein sequences. The review is divided into three main sections. In the first, commonly used terms are defined and the methods behind the databases are briefly described; in the second, the structure and content of the principal pattern databases are discussed; and in the final part, several alignment databases, which are frequently confused with pattern databases, are mentioned. For the new-comer, the array of resources, the range of methods behind them and the different tools required to search them can be confusing. The review therefore also briefly mentions a current international endeavour to integrate the diverse databases, which effort should facilitate sequence analysis in the future. This is particularly important for target-discovery programmes, where the challenge is to rationalise the enormous numbers of potential targets generated by sequence database searches. This problem may be addressed, at least in part, by reducing search outputs to the more focused and manageable subsets suggested by searches of integrated groups of family-specific pattern databases.

Amino Acid Motifs↗

PubMed1999

The PIR-International Protein Sequence Database.

The Protein Information Resource (PIR; http://www-nbrf.georgetown. edu/pir/) supports research on molecular evolution, functional genomics, and computational biology by maintaining a comprehensive, non-redundant, well-organized and freely available protein sequence database. Since 1988 the database has been maintained collaboratively by PIR-International, an international association of data collection centers cooperating to develop this resource during a period of explosive growth in new sequence data and new computer technologies. The PIR Protein Sequence Database entries are classified into superfamilies, families and homology domains, for which sequence alignments are available. Full-scale family classification supports comparative genomics research, aids sequence annotation, assists database organization and improves database integrity. The PIR WWW server supports direct on-line sequence similarity searches, information retrieval, and knowledge discovery by providing the Protein Sequence Database and other supplementary databases. Sequence entries are extensively cross-referenced and hypertext-linked to major nucleic acid, literature, genome, structure, sequence alignment and family databases. The weekly release of the Protein Sequence Database can be accessed through the PIR Web site. The quarterly release of the database is freely available from our anonymous FTP server and is also available on CD-ROM with the accompanying ATLAS database search program.

Amino Acid Sequence↗

PubMed2003

Identification of adverse drug reactions in geriatric inpatients using a computerised drug database.

INTRODUCTION AND OBJECTIVE: Geriatric patients with multiple comorbidities are at high risk of experiencing an adverse drug reaction (ADR) during hospitalisation. The aim of the study was to compare the rate of ADRs as predicted by a computerised pharmacological database to the actual rate determined by direct observation in a sample of geriatric patients. STUDY DESIGN: During a 4-month period, geriatric patients were monitored using prospective observation. Patients were intensively screened for ADRs by a pharmacoepidemiological team (PET), consisting of two pharmacists and a physician. Actual ADRs detected by the PET were compared with those predicted by a computerised drug database. Furthermore, the set of actual ADRs, which resulted from drug-drug interactions (DDIs), were contrasted with potential DDIs signalled by the database. The main outcome measures were the incidence of actual ADRs. For the detection rate of the database we focused on frequent ADRs (>1% according to product information and database) and all DDIs indicated automatically by the database. RESULTS: 163 patients (121 female), mean age 79.8 +/- 7.1 years (range 60-98), were included in the study which was conducted on a geriatric rehabilitation hospital ward. The mean duration of hospitalisation was 24.3 +/- 8.4 days. Elderly patients received an average of 14.0 drugs (range 2-35) during their hospital stay. Of all patients, 60.7% experienced at least one ADR. The PET detected a total of 153 ADRs, with a mean of 0.9 ADRs per patient (range 0-5). The computerised drug database predicted an average of 309 potential ADRs for each patient; however, only 21 ADRs per patient were of high frequency. In 48% of ADR-positive patients (defined by PET) at least one of these frequent ADRs occurred.DDIs were detected by the PET in 14.7% of patients. Our database indicated a mean of 12 potential DDIs per patient. In 14 out of 24 DDI-positive patients, at least one signal indicated a real DDI. The database sensitivity was consequently 58.3%. CONCLUSION: In geriatric patients the incidence of ADRs is high. Computerised drug databases are a useful tool for detecting and avoiding ADRs. Our software, however, also produced a large number of signals that did not relate to actual ADRs found by the PET. The sheer number of these 'false' signals shows the need for refinement and optimisation of databases for daily clinical use.

Adverse Drug Reaction Reporting Systems↗

PubMed1999

Dictated versus database-generated discharge summaries: a randomized clinical trial.

BACKGROUND: Hospital discharge summaries communicate information necessary for continuing patient care. They are most commonly generated by voice dictation and are often of poor quality. The objective of this study was to compare discharge summaries created by voice dictation with those generated from a clinical database. METHODS: A randomized clinical trial was performed in which discharge summaries for patients discharged from a general internal medicine service at a tertiary care teaching hospital in Ottawa were created by voice dictation (151 patients) or from a database (142 patients). Patients had been admitted between September 1996 and June 1997. The trial was preceded by a baseline cohort study in which all summaries were created by dictation. For the database group, information on forms completed by housestaff was entered into a database and collated into a discharge summary. For the dictation group, housestaff dictated narrative letters. The proportion of patients for whom a summary was generated within 4 weeks of discharge was recorded. Physicians receiving the summary rated its quality, completeness, organization and timeliness on a 100-mm visual analogue scale. Housestaff preference was also determined. RESULTS: Patients in the database group and the dictation group were similar. A summary was much more likely to be generated within 4 weeks of discharge for patients in the database group than for those in the dictation group (113 [79.6%] v. 86 [57.0%]; p < 0.001). Summary quality was similar (mean rating 72.7 [standard deviation (SD) 19.3] v. 74.9 [SD 16.6]), as were assessments of completeness (73.4 [SD 19.8] v. 78.2 [SD 14.9]), organization (77.4 [SD 16.3] v. 79.3 [SD 17.2]) and timeliness (70.3 [SD 21.9] v. 66.2 [SD 25.6]). Many information items of interest were more likely to be included in the database-generated summaries. The database system created summaries faster and was preferred by housestaff. Dictated summaries in the baseline and randomized studies were similar, which indicated that the control group was not substantially different from the baseline cohort. INTERPRETATION: The database system significantly increased the likelihood that a discharge summary was created. Housestaff preferred the database system for summary generation. Physicians thought that the quality of summaries generated by the 2 methods was similar. The use of computer databases to create hospital discharge summaries is promising and merits further study and refinement.

Abstracting and Indexing↗

PubMed2001

Comparison of bibliographic databases for information on the rehabilitation of people with severe mental illness.

OBJECTIVE: The research sought to examine the overlap in coverage between several health-related databases, thus enabling the identification of the most important sources for searching for information on the rehabilitation of people with severe mental illness. METHODS: The literature was searched within a systematic review. Several health-related databases were retrieved (Cumulative Index to Nursing and Allied Health Literature, The Cochrane Library, MEDLINE, PsycLIT, Sociofile, and Social Science Citation Index), noting their source and comparing results retrieved from each database. FINDINGS: The total number of studies retrieved from each database varied. Almost a third of the papers retrieved from each database were unique to that source. Forty-two percent of the papers were only found in one database. Restricting a search to one database alone would miss many papers and could affect the results of a systematic review. PsycLIT was the most useful database for this topic area, containing 44% of the papers. MEDLINE, the database of first choice for many health professionals, held only 29%. CONCLUSIONS: No database was determined to be significantly more useful than any other--each warranted inclusion in the study. Reliance cannot be placed on one database alone, and other methods such as hand searching should also be used. Although this may not be new information for information professionals, it is likely to be new for health professionals and researchers who are increasingly performing their own literature searches. Information professionals have an important role to play in conveying this message to those outside their profession.

Databases, Bibliographic↗

PubMed2001

A comparison of microarray databases.

Microarray technology has become one of the most important functional genomics technologies. A proliferation of microarray databases has resulted. It can be difficult for researchers exploring this technology to know which bioinformatics systems best meet their requirements. In order to obtain a better understanding of the available systems, a survey and comparative analysis of microarray databases was undertaken. The survey included databases that are currently available, as well as databases that should become available in early 2001. Databases fall into three categories: (i) those that can be installed locally, (ii) those available for public data submission and (iii) those available for public query. Developers of microarray gene-expression databases were asked questions regarding the scope and availability of their database, its system requirements, its future compliance with MGED (Microarray Gene Expression Database) standards, and its associated analytical tools. Participants included AMAD (Stanford/Berkeley/UCSF), ArrayExpress (EBI), ChipDB (MIT/Whitehead), GeneX (NCGR), GeNet (Silicon Genetics), GeneDirector (BioDiscovery), GEO (NCBI), GXD (Jackson Laboratory), mAdb (NCI), maxdSQL (University of Manchester), NOMAD (UCSF), RAD (University of Pennsylvania) and SMD (Stanford University). Other database developers were contacted but data was not available at the time of manuscript preparation. Each database fulfils a different role, reflecting the widely varying needs of microarray users.

Animals↗

PubMed1996

Federated two-dimensional electrophoresis database: a simple means of publishing two-dimensional electrophoresis data.

While a two-dimensional electrophoresis (2-DE) database is a relatively old concept, in recent years it generated renewed interest within the 2-DE community due to two main factors: (i) The high reproducibility of the current 2-DE method allows 2-DE images to be exchanged and compared between laboratories. (ii) The recent development of faster and more powerful techniques for protein identification such as microsequencing, matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) and amino acid composition makes the production of reference protein maps and 2-DE databases cost- and time-effective. Additionally, the Internet network's current increase in popularity, combined with the rapid growth of Internet-connected laboratories, provides a straightforward means of publishing and sharing 2-DE data. While a small number of laboratories have already successfully published their data over the net, the increasing number of 2-DE database servers that are currently being set up will sooner or later require some kind of standardization. Unfortunately, standardization can be a long and cumbersome process inevitably leading to undesirable compromises. A federated database offers a simple and efficient way to publish and share 2-DE data without the need for standardization. Taking advantage of Internet protocols such as World Wide Web, they allow each laboratory to maintain their own database and to interconnect it with other similar databases through the use of active cross-references. This paper first presents guidelines for building a federated 2-DE database that may easily be followed by most laboratories. It then briefly reviews the state-of-the-art in networked 2-DE databases, and finally describes the SWISS-2DPAGE database which fully implements the concept of a federated 2-DE database.

Computer Communication Networks↗

PubMed2003

Strengthening the United States' database protection laws: balancing public access and private control.

This paper develops three arguments for increasing the strength of database protection under U.S. law. First, stronger protections would encourage private investment in database development, and private databases have many potential benefits for science and industry. Second, stronger protections would discourage extensive use of private licenses to protect databases and would allow for greater public control over database laws and policies. Third, stronger database protections in the U.S. would harmonize U.S. and E.U. laws and would thus enhance international trade, commerce, and research. The U.S. should therefore follow the European example and develop two tiers of protection for databases: 1) protection for creative databases under copyright law; 2) protection for non-creative databases through a special type of sui generis protection. In order to balance private control of data and public access to data, sui generis protections should define a "fair use" exemption that permits some unauthorized extraction of data for private, educational, and research purposes, provided that such extraction does not adversely impact the economic value of the database.

Access to Information↗

PubMed2001

Criminal DNA databases: the European situation.

In the last 5 years, a number of European countries have successfully introduced national databases holding the DNA profiles from suspected and convicted criminal offenders as well as from biological stain materials from unsolved crime cases. At present, DNA databases are fully or partially in operation in the UK, The Netherlands, Austria, Germany, Finland, Norway, Denmark, Switzerland and Sweden. Furthermore, in the other European countries, specific legislation will be enacted soon, or the introduction of such databases is being discussed to initiate a legislative process. Numerous differences exist regarding the criteria for a criminal offender to be included in the database, the storage periods and the possibility to remove database records, the possibility to keep reference samples from the offenders as long as their respective records are being held, and the role of judges in the process of entering a database record or to perform a database search. Nevertheless, harmonization has been achieved regarding the DNA information stored in national databases, and a European standard set of genetic systems has been recommended which is included either in part or completely in the DNA profiles of offenders and crime stains for all European databases. This facilitates the exchange of information from database records to allow the investigation of crime cases across national borders.

Confidentiality↗

PubMed2003

Database system, AFoDas/AVODAS, on indoor air organic compounds in Japan. Automated Formaldehyde Data Acquisition System. Automated VOC Data Acquisition System.

Building designers, engineers and occupants often need to estimate the organic compounds' levels in buildings. In order to satisfy the requirement, a web-based database, named AFoDAS/AVODAS database system is developed. The database consists of six databases for managing indoor air organic compounds' levels and building's environmental conditions. The database includes the monitoring results of about 1422 homes. The database allows users to (1) input their monitoring results to the database; (2) browse, search and query the database by a single or combinations of criteria for various query parameters such as building category, ventilation system, environment category, and compound names; and (3) estimate the organic compounds' levels resulting from various buildings and environmental conditions. This paper describes the functionality, database structure and major features of the user interface system of the database.

Air Pollution, Indoor↗