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The use of federal and state databases to conduct health services research related to physical and occupational therapy.

OBJECTIVE: To describe the characteristics of a number of secondary databases that have the potential to answer questions related to the use of, access to, and effectiveness of physical therapy (PT) and occupational therapy (OT). DATA SOURCES: Federal and state databases maintained by the National Center for Health Statistics, the Agency for Healthcare Research and Quality, and the Centers for Medicare and Medicaid Services. STUDY SELECTION: Databases, described above, that were identified as having potential for answering questions related to the use and effectiveness of PT and OT were examined. DATA EXTRACTION: The databases were explored to determine if PT and OT had sufficient representation, and if so, to identify potential questions that could be answered by examining the databases in more detail. Some of the advantages, disadvantages, and methodologic issues of using the databases were identified. DATA SYNTHESIS: Several databases are available that can be used by researchers to increase our understanding of the use of, access to, and/or effectiveness of PT and OT. Many of the databases are most suited for examining issues related to the use of and access to these services. A few of the databases can be used to examine the effectiveness of PT and OT. CONCLUSION: Secondary data analyses are a particularly useful, cost-effective, and efficient means for preliminary exploration of topics that are not well understood, such as the use of, access to, and effectiveness of PT and OT.

Data Collection↗

Randomized sequence databases for tandem mass spectrometry peptide and protein identification.

Tandem mass spectrometry (MS/MS) combined with database searching is currently the most widely used method for high-throughput peptide and protein identification. Many different algorithms, scoring criteria, and statistical models have been used to identify peptides and proteins in complex biological samples, and many studies, including our own, describe the accuracy of these identifications, using at best generic terms such as "high confidence." False positive identification rates for these criteria can vary substantially with changing organisms under study, growth conditions, sequence databases, experimental protocols, and instrumentation; therefore, study-specific methods are needed to estimate the accuracy (false positive rates) of these peptide and protein identifications. We present and evaluate methods for estimating false positive identification rates based on searches of randomized databases (reversed and reshuffled). We examine the use of separate searches of a forward then a randomized database and combined searches of a randomized database appended to a forward sequence database. Estimated error rates from randomized database searches are first compared against actual error rates from MS/MS runs of known protein standards. These methods are then applied to biological samples of the model microorganism Shewanella oneidensis strain MR-1. Based on the results obtained in this study, we recommend the use of use of combined searches of a reshuffled database appended to a forward sequence database as a means providing quantitative estimates of false positive identification rates of peptides and proteins. This will allow researchers to set criteria and thresholds to achieve a desired error rate and provide the scientific community with direct and quantifiable measures of peptide and protein identification accuracy as opposed to vague assessments such as "high confidence."

Databases, Protein↗

PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2.

SUMMARY: PICRUSt2 is a bioinformatic tool that predicts microbial functions in amplicon sequencing data using a database of annotated reference genomes. We have constructed an updated database for PICRUSt2 that has substantially increased the number of bacterial (19,493 to 26,868) and archaeal (406 to 1,002) genomes as well as the number of functional annotations present. The previous PICRUSt2 database relied on many timely and computationally intensive manual processes that made it difficult to update. We constructed a new streamlined process to allow regular upgrades to the PICRUSt2 database on an ongoing basis, and used this process to create a new database, PICRUSt2-SC (Sugar-Coated). Additionally, we have shown that this updated database contains genomes that more closely match study sequences from a range of different environments. The genomes contained in the database therefore better represent these environments and this leads to an improvement in the predicted functional annotations obtained from PICRUSt2. AVAILABILITY AND IMPLEMENTATION: PICRUSt2 source code is freely available at https://github.com/picrust/picrust2 and at https://anaconda.org/bioconda/picrust2. The latest version of PICRUSt2 at the time of writing is also archived: https://doi.org/10.5281/zenodo.15119781. The PICRUSt2-SC database comes pre-installed with PICRUSt2 from version 2.6.0 onwards. Step-by-step instructions for making the updated database are at https://github.com/picrust/picrust2/wiki/Updating-the-PICRUSt2-database. All code used for the analyses and figures in this manuscript is at https://github.com/R-Wright-1/PICRUSt2-SC_application_note and https://doi.org/10.5281/zenodo.15119770.

Software↗

Databases and software for the analysis of mutations in the human p53 gene, the human hprt gene and the lacZ gene in transgenic rodents.

We have created databases and software applications for the analysis of DNA mutations in the human p53 gene, the human hprt gene and the rodent transgenic lacZ locus. The databases themselves are stand-alone dBase files and the software for analysis of the databases runs on IBM- compatible computers. The software created for these databases permits filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web (WWW). Open home page http://sunsite.unc.edu/dnam/mainpage.ht ml with a WWW browser. Alternatively, the databases and programs are available via public ftp from anonymous@sunsite.unc.edu. There is no password required to enter the system. The databases and software are found in subdirectory pub/academic/biology/dna-mutations. Two other programs are available at the WWW site, a program for comparison of mutational spectra and a program for entry of mutational data into a relational database.

Animals↗

MIPS: a database for genomes and protein sequences.

The Munich Information Center for Protein Sequences (MIPS-GSF), Martinsried, near Munich, Germany, continues its longstanding tradition to develop and maintain high quality curated genome databases. In addition, efforts have been intensified to cover the wealth of complete genome sequences in a systematic, comprehensive form. Bioinformatics, supporting national as well as European sequencing and functional analysis projects, has resulted in several up-to-date genome-oriented databases. This report describes growing databases reflecting the progress of sequencing the Arabidopsis thaliana (MATDB) and Neurospora crassa genomes (MNCDB), the yeast genome database (MYGD) extended by functional analysis data, the database of annotated human EST-clusters (HIB) and the database of the complete cDNA sequences from the DHGP (German Human Genome Project). It also contains information on the up-to-date database of complete genomes (PEDANT), the classification of protein sequences (ProtFam) and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database. These databases can be accessed through the MIPS WWW server (http://www. mips.biochem.mpg.de).

Arabidopsis↗

Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003.

The Rice Proteome Database is the first detailed database to describe the proteome of rice. The current release contains 21 reference maps based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of proteins from rice tissues and subcellular compartments. These reference maps comprise 11 941 identified proteins showing tissue and subcellular localization, corresponding to 4180 separate protein entries in the database. The Rice Proteome Database contains the calculated properties of each protein such as molecular weight, isoelectric point and expression; experimentally determined properties such as amino acid sequences obtained using protein sequencers and mass spectrometry; and the results of database searches such as sequence homologies. The database is searchable by keyword, accession number, protein name, isoelectric point, molecular weight and amino acid sequence, or by selection of a spot on one of the 2D-PAGE reference maps. Cross-references are provided to tools for proteomics and to other 2D-PAGE databases, which in turn provide many links to other molecular databases. The information in the Rice Proteome Database is updated weekly, and is available on the World Wide Web at http://gene64.dna.affrc.go.jp/RPD/.

Computational Biology↗

The EMBL Nucleotide Sequence Database.

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/), maintained at the European Bioinformatics Institute (EBI), incorporates, organizes and distributes nucleotide sequences from public sources. The database is a part of an international collaboration with DDBJ (Japan) and GenBank (USA). Data are exchanged between the collaborating databases on a daily basis to achieve optimal synchrony. The web-based tool, Webin, is the preferred system for individual submission of nucleotide sequences, including Third Party Annotation (TPA) and alignment data. Automatic submission procedures are used for submission of data from large-scale genome sequencing centres and from the European Patent Office. Database releases are produced quarterly. The latest data collection can be accessed via FTP, email and WWW interfaces. The EBI's Sequence Retrieval System (SRS) integrates and links the main nucleotide and protein databases as well as many other specialist molecular biology databases. For sequence similarity searching, a variety of tools (e.g. FASTA and BLAST) are available that allow external users to compare their own sequences against the data in the EMBL Nucleotide Sequence Database, the complete genomic component subsection of the database, the WGS data sets and other databases. All available resources can be accessed via the EBI home page at http://www.ebi.ac.uk.

Animals↗

The Molecular Biology Database Collection: 2006 update.

The NAR Molecular Biology Database Collection is a public online resource that contains links to all databases described in this issue of Nucleic Acids Research. In addition, this collection lists databases that have been featured in previous issues of NAR, as well as selected other databases that are freely available to the public and may be useful to the molecular biologist. The 2006 update includes 858 databases, 139 more than the previous one. The databases come with brief summaries, many of which have been updated recently. Each database is assigned a stable accession number that does not change if the database moves to a new location and its URL, authors' names or the contact person address are updated. The complete database list and summaries are available online at the Nucleic Acids Research website http://nar.oxfordjournals.org/.

Databases, Genetic↗

A decade's experience with quality improvement in cardiac surgery using the Veterans Affairs and Society of Thoracic Surgeons national databases.

OBJECTIVE: To review the Department of Veteran Affairs (VA) and the Society of Thoracic Surgeons (STS) national databases over the past 10 years to evaluate their relative similarities and differences, to appraise their use as quality improvement tools, and to assess their potential to facilitate improvements in quality of cardiac surgical care. SUMMARY BACKGROUND DATA: The VA developed a mandatory risk-adjusted database in 1987 to monitor outcomes of cardiac surgery at all VA medical centers. In 1989 the STS developed a voluntary risk-adjusted database to help members assess quality and outcomes in their individual programs and to facilitate improvements in quality of care. METHODS: A short data form on every veteran operated on at each VA medical center is completed and transmitted electronically for analysis of unadjusted and risk-adjusted death and complications, as well as length of stay. Masked, confidential semiannual reports are then distributed to each program's clinical team and the associated administrator. These reports are also reviewed by a national quality oversight committee. Thus, VA data are used both locally for quality improvement and at the national level with quality surveillance. The STS dataset (217 core fields and 255 extended fields) is transmitted for each patient semiannually to the Duke Clinical Research Institute (DCRI) for warehousing, analysis, and distribution. Site-specific reports are produced with regional and national aggregate comparisons for unadjusted and adjusted surgical deaths and complications, as well as length of stay for coronary artery bypass grafting (CABG), valvular procedures, and valvular/CABG procedures. Both databases use the logistic regression modeling approach. Data for key processes of care are also captured in both databases. Research projects are frequently carried out using each database. RESULTS: More than 74,000 and 1.6 million cardiac surgical patients have been entered into the VA and STS databases, respectively. Risk factors that predict surgical death for CABG are very similar in the two databases, as are the odds ratios for most of the risk factors. One major difference is that the VA is 99% male, the STS 71% male. Both databases have shown a significant reduction in the risk-adjusted surgical death rate during the past decade despite the fact that patients have presented with an increased risk factor profile. The ratio of observed to expected deaths decreased from 1.05 to 0.9 for the VA and from 1.5 to 0.9 for the STS. CONCLUSION: It appears that the routine feedback of risk-adjusted data on local performance provided by these programs heightens awareness and leads to self-examination and self-assessment, which in turn improves quality and outcomes. This general quality improvement template should be considered for application in other settings beyond cardiac surgery.

Cardiac Surgical Procedures↗

Research potentials and pitfalls in the use of an HIV clinical database: Chelsea and Westminster Hospital.

This article summarizes the various problems and pitfalls in using clinical databases for epidemiologic research, with particular reference to an HIV clinical database. The combined population of HIV-infected individuals attending the Chelsea and Westminster Hospital, the Charing Cross Hospital, and the Victoria Clinic in London is the largest cohort of HIV-positive individuals in the U.K. A computerized database was developed in the mid-1980s and was adapted into a clinically oriented observational database for approximately 6,653 HIV-1-positive registered patients from three hospital-based clinics within the Riverside Health Authority in London, U.K.: Chelsea and Westminster Hospital Clinic (n = 5,000); Charing Cross Hospital (n = 500); and the Victoria Clinic (n = 500). The majority (83%) of HIV-infected patients registered at these sites are homosexual or bisexual men. Of 2,078 patients seen within the last 6 months, 22% are asymptomatic and 33% have AIDS; 30% have a CD4 cell count of less than 100 cells/mm3 and 17% have a CD4 cell count of greater than 500 cells/mm3. Dates of seroconversion are known for approximately 285 patients. For each patient, information on demographic characteristics, clinical symptoms, and HIV-related diagnoses, outpatient pharmacy prescriptions, day care treatments and procedures, and enrollment into clinical trials is routinely collected at outpatient clinic visits and entered into the database. Inpatient diagnoses and treatments were integrated into the database in September 1995. Unused serum samples from routine AIDS antibody or antigen testing are stored in a local specimen repository. The main purpose of the HIV database is to provide a multipurpose resource for use by physicians, researchers, and managers for administration, clinical care, and research. The specific functions of the database are the following: to enhance patient management by providing access to a clinical summary sheet detailing up-to-date information; to serve as a research tool for clinical and epidemiologic research; to aid in the identification of patients eligible for planned or ongoing clinical trials; to provide a facility for local and regional AIDS surveillance and reporting; and to provide a facility for administration and resource management of HIV services. The major limitations of this database in the conduct of clinical research have been losses to follow-up and incomplete information about clinical outcomes, because physicians have failed to update the clinical information.

Acquired Immunodeficiency Syndrome↗

The validity of diagnosing chronic obstructive pulmonary disease from a large administrative database.

BACKGROUND: Health authorities create and maintain administrative databases. Despite the potential advantages of these databases, the validity of the information they include must be considered. OBJECTIVE: To examine the validity of diagnosing chronic obstructive pulmonary disease (COPD) from a large administrative database. METHODS: Physician services and prescription claims data related to COPD and asthma were extracted from the Quebec universal medical insurance register (Régie de l'assurance-maladie du Québec; RAMQ) from the period of April 1, 1994 to March 31, 1999. Before obtaining the data, criteria for the validity of the COPD diagnosis in the database were formulated based on the epidemiology of COPD in the province. The extent to which the database satisfied these criteria are described within the present paper. RESULTS: For patients aged 65 years or older, COPD was two times more prevalent in the RAMQ database than in the 1994/1995 National Population Health Survey. One in three patients with a RAMQ-diagnosis of COPD also had a RAMQ-diagnosis of asthma, and 47% of patients aged 65 years or older with a RAMQ-diagnosis of COPD did not fill any prescription for beta-2-agonists. In addition, 42% of patients with a RAMQ-diagnosis of COPD who never had a RAMQ-diagnosis of asthma appeared only once with that diagnosis in the database. Of all patients aged 65 years or older with a RAMQ-diagnosis of COPD, 37% and 23% met the operational definitions of 'possible COPD' and 'probable COPD', respectively. CONCLUSIONS: Most RAMQ-diagnoses of COPD lack validity; therefore, the validity of database diagnoses should be routinely ascertained before using administrative databases in clinical and health services research.

Adult↗

CED: a conformational epitope database.

BACKGROUND: Antigen epitopes provide valuable information useful for disease prevention, diagnosis, and treatment. Recently, more and more databases focusing on different types of epitopes have become available. Conformational epitopes are an important form of epitope formed by residues that are sequentially discontinuous but close together in three-dimensional space. These epitopes have implicit structural information, making them attractive for both theoretical and applied biomedical research. However, most existing databases focus on linear rather than conformational epitopes. DESCRIPTION: We describe CED, a special database of well defined conformational epitopes. CED provides a collection of conformational epitopes and related information including the residue make up and location of the epitope, the immunological property of the epitope, the source antigen and corresponding antibody of the epitope. All entries in this database are manually curated from articles published in peer review journals. The database can be browsed or searched through a user-friendly web interface. Most epitopes in CED can also be viewed interactively in the context of their 3D structures. In addition, the entries are also hyperlinked to various databases such as Swiss-Prot, PDB, KEGG and PubMed, providing wide background information. CONCLUSION: A conformational epitope database called CED has been developed as an information resource for investigators involved in both theoretical and applied immunology research. It complements other existing specialised epitope databases. The database is freely available at http://web.kuicr.kyoto-u.ac.jp/~ced.

Animals↗

A relational database for diagnosis of hematopoietic neoplasms using immunophenotyping by flow cytometry.

A relational database was developed to facilitate the diagnosis of hematopoietic neoplasms using results of immunophenotyping by flow cytometry. This database runs on personal computers and uses backward-chaining search to arrive at conclusions. Results of immunologic marker studies are processed by the database to obtain a set of differential diagnoses. The current version of this database includes diagnostic immunophenotyping pattern for 33 hematopoietic neoplasms. We tested this database using 92 clinical cases from 2 tertiary care medical centers. The database ranked the actual diagnosis as 1 of the top 5 differential diagnoses in 93% of the cases tested. The user can modify the database contents to suit individual needs. This database has been posted on the World Wide Web for direct access. We propose that this user-friendly database is a potential tool for computer-assisted diagnosis of hematopoietic neoplasms.

Antigens, CD↗

Identifying the active general practice workforce in one division of general practice: the utility of public domain databases.

OBJECTIVE: To identify the non-specialist medical practitioner workforce engaged in active general practice in the region served by the Division of General Practice-Northern Tasmania and to determine the usefulness of public domain databases for enumeration of individual non-specialists providing general practice services. METHODS: A masterlist of the active general practice workforce was compiled by obtaining the names and addresses/postcodes of all non-specialist medical practitioners who were listed in at least one of nine public domain databases and who were confirmed by selected local medical practitioners to be in active general practice in the three months prior to 30 June 1994. This masterlist was used in calculating the sensitivity and positive predictive value (PPV) of each of the nine databases for enumerating non-specialist practitioners in active general practice. RESULTS: Combining the databases resulted in a list of 475 practitioners, which was refined to 139 practitioners who, by our criteria, were in active general practice. Databases had a range of sensitivities and PPVs, but those with high sensitivity tended to have low PPVs, and vice versa. The most useful database for enumerating these practitioners was the mailing list for Australian Family Physician (sensitivity, 94%; PPV, 0.79). CONCLUSIONS: When used alone, no single database had both high sensitivity and high positive predictive value for identifying the active general practice workforce. Combining multiple databases may improve precision. Developing methods to identify recent departures from local active practice has the potential to improve the PPV of existing highly sensitive databases.

Australia↗

Comparison of literature searches on quality and costs for health technology assessment using the MEDLINE and EMBASE databases.

Biomedical databases are an important source of information for health technology assessment. However, there is considerable variation in the costs of accessing commercial databases. We sought to measure the quality, amount of overlap, and costs of information retrieved from two of the main database sources--MEDLINE and EMBASE. Librarians at two health technology assessment agencies ran a total of eight literature searches on various medical technologies, using both databases. All search results were independently reviewed by two researchers. The researchers were asked to identify relevant references and to rank each of these according to a level of evidence scale. The results were tabulated to show the number of references identified by each database, the number of relevant references ranked by level of evidence, and the number of these references that were unique to one or the other database. The cost of retrieving references from each source was also calculated. Each database contained relevant references not available in the other. Because of the longer time lag for indexing in MEDLINE, many of the references that originally appeared to be unique to EMBASE were subsequently available in MEDLINE as well. Since our study was conducted, MEDLINE has been made available worldwide, free of charge, via the Internet. Hence, the cost difference between the databases is now even greater. However, notwithstanding the costs, it appears that literature searches that rely on only one or the other database will inevitably miss pertinent information.

Abstracting and Indexing↗

[The ZEBET database on alternative methods to animal experiments in the Internet--a concrete contribution to the protection of animals].

Up from February of the year 2000 ZEBET (German Centre for the Documentation and Validation of Alternative Methods) at the Federal Institute for Consumer Health Protection and Veterinary Medicine (BgVV) put the ZEBET-database on alternative methods to animal experiments on the Internet in English via DIMDI, the German Institute for Medical Documentation and Information (http://gripsdb.dimdi.de/engl/guieng.html). The access is free, moreover DIMDI's complete service is available to visitors of the ZEBET-database. The ZEBET database contains documents on alternatives to testing in animals, which have been carefully evaluated by ZEBET's staff according to the "3Rs"-concept established by Russel and Burch in 1959. Therefore, methods documented in the ZEBET database must meet at least one of the following criteria: "replacement" of an animal experiment by a non-animal method, "reduction" of the number of animals used, "refinement" of an experiment by minimising pain and suffering of animals. In addition, the ZEBET-database provides information on the current stage of development and validation of a method and on the acceptance for either scientific or regulatory purposes. Each document is characterised by the following criteria: the title of a method, keywords, assessment, summary and bibliographic references. To search DIMDI<<s-database and host-system the grips software has to be used. Examples are given for searching in the ZEBET-database. Currently 125 alternative methods are meeting the criteria of the ZEBET database. 50 of them are available online on the internet via DIMDI, the remaining 75 documents will be available by the end of the year 2000. International fellow organisations, e.g. FRAME (Fund for the Replacement of Animals in Medical Experiments) in the UK and CAAT (Johns Hopkins Center for Alternatives to Animal Testing) in the USA, have established links on their web sites to provide visitors free access to the ZEBET-database.

Animal Testing Alternatives↗

Answering family physicians' clinical questions using electronic medical databases.

OBJECTIVE: We studied the ability of electronic medical databases to provide adequate answers to the clinical questions of family physicians. STUDY DESIGN: Two family physicians attempted to answer 20 questions with each of the databases evaluated. The adequacy of the answers was determined by the 2 physician searchers, and an arbitration panel of 3 family physicians was used if there was disagreement. DATA SOURCE: We identified 38 databases through nominations from national groups of family physicians, medical informaticians, and medical librarians; 14 met predetermined eligibility criteria. OUTCOMES MEASURED: The primary outcome was the proportion of questions adequately answered by each database and by combinations of databases. We also measured mean and median times to obtain adequate answers for individual databases. RESULTS: The agreement between family physician searchers regarding the adequacy of answers was excellent (k=0.94). Five individual databases (STAT!Ref, MDConsult, DynaMed, MAXX, and MDChoice.com) answered at least half of the clinical questions. Some combinations of databases answered 75% or more. The average time to obtain an adequate answer ranged from 2.4 to 6.5 minutes. CONCLUSION: Several current electronic medical databases could answer most of a group of 20 clinical questions derived from family physicians during office practice. However, point-of-care searching is not yet fast enough to address most clinical questions identified during routine clinical practice.

Clinical Competence↗

Spanish personal name variations in national and international biomedical databases: implications for information retrieval and bibliometric studies.

OBJECTIVES: The study sought to investigate how Spanish names are handled by national and international databases and to identify mistakes that can undermine the usefulness of these databases for locating and retrieving works by Spanish authors. METHODS: The authors sampled 172 articles published by authors from the University of Granada Medical School between 1987 and 1996 and analyzed the variations in how each of their names was indexed in Science Citation Index (SCI), MEDLINE, and Indice Medico Español (IME). The number and types of variants that appeared for each author's name were recorded and compared across databases to identify inconsistencies in indexing practices. We analyzed the relationship between variability (number of variants of an author's name) and productivity (number of items the name was associated with as an author), the consequences for retrieval of information, and the most frequent indexing structures used for Spanish names. RESULTS: The proportion of authors who appeared under more then one name was 48.1% in SCI, 50.7% in MEDLINE, and 69.0% in IME. Productivity correlated directly with variability: more than 50% of the authors listed on five to ten items appeared under more than one name in any given database, and close to 100% of the authors listed on more than ten items appeared under two or more variants. Productivity correlated inversely with retrievability: as the number of variants for a name increased, the number of items retrieved under each variant decreased. For the most highly productive authors, the number of items retrieved under each variant tended toward one. The most frequent indexing methods varied between databases. In MEDLINE and IME, names were indexed correctly as "first surname second surname, first name initial middle name initial" (if present) in 41.7% and 49.5% of the records, respectively. However, in SCI, the most frequent method was "first surname, first name initial second name initial" (48.0% of the records) and first surname and second surname run together, first name initial (18.3%). CONCLUSIONS: Retrievability on the basis of author's name was poor in all three databases. Each database uses accurate indexing methods, but these methods fail to result in consistency or coherence for specific entries. The likely causes of inconsistency are: (1) use by authors of variants of their names during their publication careers, (2) lack of authority control in all three databases, (3) the use of an inappropriate indexing method for Spanish names in SCI, (4) authors' inconsistent behaviors, and (5) possible editorial interventions by some journals. We offer some suggestions as to how to avert the proliferation of author name variants in the databases.

Databases, Bibliographic↗