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PubMed1995

Quality initiatives and the power of the database: what they are and how they run.

The criteria by which healthcare is judged or measured are quality, accessibility, and cost effectiveness. To evaluate these criteria it is important to have a database. There are many strengths and weakness to large databases. They can be used as an indicator of the level of performance or quality, for clinical decision making, and as a measurement of cost effectiveness. They can also be useful in the evaluation and development of treatment algorithms and critical pathways for patients with entry level disease. In addition, they can measure patient access to healthcare and the appropriateness of care. It is important for these databases to appropriately adjust for preoperative risk factors that may influence outcome. Outcome in most of the databases is measured by mortality, but morbidity, functional status, quality of life, cost of care, length of stay, return to work, and patient satisfaction are also important outcomes. Factors that can influence the quality of the outcome data are the methods by which the data are collected, standardization of definitions, the currentness of the database, adequate numbers of patients and outcomes, and appropriate analytic techniques. It is important to feed back the data to the healthcare providers in a timely enough fashion so that processes and structures of care can be modified to improve treatment and results. The reliability of the databases and the validity must be substantiated for the healthcare provider to have confidence in the database.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗
PubMed1992

The free form database program as a research tool.

Two types of database programs for the IBM compatible personal computer (PC) are described: the fixed form database and the free form database. The use of the latter in compiling bibliographic databases and in content analysis of interview transcripts is described. Other uses for the free form database program are also discussed. It is suggested that the free form database has advantages over some other custom-made analysis programs in terms of its simplicity and ease of use. It is also suggested that the free form database can be a useful tool for nurse educators and students.

Databases, Bibliographic↗
PubMed2004

Are unaudited records from an outcomes registry database accurate?

BACKGROUND: Data from outcomes registry databases are being increasingly used for peer review and public reporting. However, administrative and clinical databases are mostly unaudited; thus, their accuracy has not been verified. METHODS: Outcomes data from all coronary artery bypass operations from a single cardiac surgery practice were entered into The Society of Thoracic Surgeons (STS) National Cardiac Database. From our practice of 18 surgeons, we audited 247 (10%) of the clinical records of patients undergoing surgery in 2001 and correlated them with all 315 elements of the STS National Cardiac Database for verification of accuracy. Inaccuracies were defined as a disagreement with a nominal or categorical variable or, for continuous variables, as the value not being within a predetermined window. When discrepancies existed, the hospital clinical record was assumed to be accurate. Outcomes discrepancies were then analyzed by four major categories: components of the preoperative risk algorithm, operative mortality, major complications, and other outcomes. RESULTS: Discrepancies were noted in 5% (16) or fewer of the audited fields for 98.8% of the records. Of the 32 variables in the mortality risk algorithms, discrepancies were present in fewer than 10% of the audits on 30 of the 32 variables. More than 95% of the audited charts had zero or one discrepancy in the seven most important variables in the mortality risk models. Operative mortality was determined to be completely accurate with no discrepancies between the database and the audited clinical record. Among major complications, the error rate was less than 1% for all complications except prolonged ventilation (4.0%). A higher rate of discrepancies did exist in some of the other variables, including discharge medications (14.1%) and ventilator time (36.4%). CONCLUSIONS: A detailed audit of a clinical outcomes registry database demonstrated that the major fields within this specific database including operative mortality, major complications, and the significant factors in the risk algorithm were highly accurate. Process improvement factors were identified to further increase the accuracy of data collection.

Cardiac Surgical Procedures↗
PubMed2005

Establishment of tyrosinase sequence database in normally pigmented Indians and Japanese for rapid determination of novel mutations.

BACKGROUND: Many mutations of the tyrosinase gene have been reported in oculocutaneous albinism type I (OCA1) patient. In the future, a greater number of novel mutations will be found as the search for pathological mutations in the tyrosinase genes of OCA patients from various ethnic origins. For rapid determination in future whether an observed mutation is a polymorphism or a novel pathological one, sequence databases of the gene of various ethnic people are needed. OBJECTIVE: We established a sequence database of the tyrosinase gene of Japanese as well as Indian people. METHOD: We collected DNA from 109 Japanese and 103 Indians with normal pigmentation and analyzed their tyrosinase gene using a direct sequencing method. RESULT: The database shows an apparent difference between the two ethnic groups in polymorphisms of the tyrosinase gene namely, Q402 allele, Y192 allele and IV2+24 insT were found in the Indian population, but not in the Japanese. On the other hand, some Japanese had IV2-21 insT but none of the Indians did. The database supports the notion that the tyrosinase gene evolved and extended separately in the two ethnic groups. And the developing database confirmed that the reported mutations causing Indian and Japanese OCA were not among the polymorphisms in the database, which conversely gives genetical proof of the "genuine" pathological mutations. CONCLUSION: Eventually, the sequence database we established will contribute to demonstrating novel mutations of albinism in Indians and Japanese.

Albinism, Ocular↗
PubMed2004

Compilation of a MALDI-TOF mass spectral database for the rapid screening and characterisation of bacteria implicated in human infectious diseases.

A database of MALDI-TOF mass spectrometry (MS) profiles has been developed with the aim of establishing a high throughput system for the characterisation of microbes. Several parameters likely to affect the reproducibility of the mass spectrum of a taxon were exhaustively studied. These included such criteria as sample preparation, growth phase, culture conditions, sample storage, mass range of ions, reproducibility between instruments and the methodology prior to database entry. Replicates of 12 spectra per sample were analysed using a 96-well target plate containing central wells for peptide standards to correct against mass drift during analysis. The quality of the data was assessed statistically prior to database addition using root mean squared values of <3.0 as the criterion for rejection. Cluster analysis using a nearest neighbour algorithm also enabled subsets of data to be compared. This was achieved using the bespoke MicrobeLynx trade mark software. Columbia blood agar was used to standardise all procedures for the database, since it permitted the culture of most human pathogens and also produced spectra with a broad range of mass ions. In some instances, alternative media such as CLED were used in specific studies with greater success. Following standardisation of the procedure, a database was developed comprising ca. 3500 spectra with multiple strain entries for most species. The results to date show unequivocally that as the number of strains per species increased, so too did the success of species matching. The technique demonstrated unique mass spectral profiles for each genus/species, with the variation in mass ions among strains/species being dependent on the intra-specific diversity. The success of identification against the database for wild-type strains ranged between 33 and 100%; the lower percentage results being generally associated with poor representation of some species within the database. These findings provide a new dimension for the rapid and high throughput characterisation of human pathogens with potentially broad applications across the field of microbiology.

Algorithms↗
PubMedDate not supplied

Quantitative Tc-99m sestamibi attenuation-corrected SPECT: development and multicenter trial validation of myocardial perfusion stress gender-independent normal database in an obese population.

BACKGROUND: A gender-independent stress normal database and criteria for abnormality for attenuation-corrected rest-stress technetium 99m sestamibi same-day myocardial perfusion imaging were developed by evaluation of 112 patients, validated against an obese population of 95 patients from four different clinical sites, and compared with conventional gender-matched database quantification of non-attenuation-corrected studies. METHODS AND RESULTS: These 95 validation patients (63 men) were used for prospective quantitative evaluation (mean weight, 213 +/- 57 lb; mean body mass index, 32 +/- 9 kg/m(2)). This group included 21 patients (12 men) with a lower than 5% likelihood of coronary artery disease (mean weight, 226 +/- 72 lb; mean body mass index, 34 +/- 13 kg/m(2)) and 74 who underwent cardiac catheterization within 2 months (35 with normal coronaries or coronary lesions <70%). These studies were processed twice, once by use of conventional reconstruction and gender-specific database quantification and a second time by use of attenuation correction and a single gender-independent attenuation-corrected normal database. The attenuation-corrected normal database and criteria for abnormality were developed by evaluation of 48 and 78 patients, respectively. No statistically significant differences were found when comparing attenuation-corrected perfusion distributions of normal men and women, whereas significant differences were found in the same uncorrected studies. Compared with quantitative analysis of the uncorrected studies, quantitative analysis of the attenuation-corrected studies by use of a gender-independent normal database demonstrated a significant improvement in normalcy rate (90% vs 52%, P =.006) and specificity (57% vs 29%, P =.015) in this obese population at no significant loss in sensitivity (90% vs 97%, P = not significant). CONCLUSION: Attenuation-corrected studies can be quantified with a single gender-independent normal database and a single criterion for abnormality without loss of sensitivity and with significantly better specificity and normalcy rate.

Coronary Artery Disease↗
PubMed2004

Conditioned taste aversion: a database.

The present commentary describes the availability of a database on conditioned taste aversion learning, the avoidance of fluids and foods previously associated with the aversive effects of a variety of drugs. The database includes articles as early as 1955 by Garcia and his colleagues [Science 122 (1955) 127] (reporting such avoidance in rats) and papers just published given that the database is ongoing and constantly updated. At the printing of this announcement, approximately 2600 papers are included in the database. The database allows the user to search for articles by author(s), key word(s), date, title and journal. These terms can be used as single entries or multiple combinations. Finally, the full database can be viewed by performing the search function without entering any terms in the query window. The database can be accessed at http://www.CTALearning.com.

Animals↗
PubMed2006

ChickGCE: a novel germ cell EST database for studying the early developmental stage in chickens.

We established a database to study germ cells during the early developmental stage in the chicken. The ChickGCE database provides integrated expressed sequence tag (EST) data from chicken testis, ovary, embryonic gonads, and primordial germ cells. We gathered data on 10,294 ESTs from approximately 1000 embryonic gonads, and we experimentally determined 10,851 ESTs from primordial germ cells purified from 7955 embryonic gonads by magnetically activated cell sorting. The EST testis and ovary datasets were retrieved from the public database of The Institute for Genomic Research (TIGR). The EST data were clustered and assembled into unique sequences, contigs, and singletons. The ChickGCE database provides functional annotation, identification, and putative embryonic germ-cell-specific novel transcripts based on the Gene Ontology database, as well as statistical analyses of expression patterns and pair-wise comparisons of two types of tissue- and germ-cell-specific alternative splicing events in the chicken. The new database is accessible online and queries can be answered using several search options, including tissue database searches, keywords, clone IDs, expected values, and BLAST search scores.

Animals↗
PubMed2001

Relational database structure to manage high-density tissue microarray data and images for pathology studies focusing on clinical outcome: the prostate specialized program of research excellence model.

With the completion of the Human Genome Project and high-throughput screening methods using cDNA array and tissue microarray (TMA) technology, there is a pressing need to manage the voluminous data sets generated from these types of investigations. Herein is described a database model to handle 1) clinical and pathology data, 2) TMA location information, and 3) web-based histology results. The model is useful for managing clinical, pathology, and molecular data on >1300 prostate cancer patients dating back to 1995 from the University of Michigan Specialized Program of Research Excellence for prostate cancer. The key components in this multidatabase model are 1) the TMA database, 2) the TMA-image database (TMA-I DB), and 3) the prostate pathology and clinical information databases. All databases were created in Microsoft Access (Microsoft, Redmond, WA). Desired patient, tissue, block, diagnosis, array location, and respective clinical and pathology information is obtained by linking the unique identifier fields among database tables. The TMA database is comprised of interrelated data from 336 prostate cancer patients transferred into 19 TMA blocks with 5451 TMA biopsy cores. Tissue samples include 1695 normal prostate, 3171 prostate cancer, 464 prostatic intraepithelial neoplasia, and 121 atrophy. All 19 TMA blocks have been analyzed over the Internet for several immunohistochemical biomarkers including E-cadherin, prostate-specific antigen, p27(Kip1), and Ki-67 labeling index. This system facilitates the statistical analysis of high-density TMA data with clinical and pathology information in an efficient and cost-effective manner. Because the review is performed over the Internet, this system is ideal for collaborative multi-institutional studies.

Databases as Topic↗
PubMed2001

Do the research goal and databases match? A checklist for a systematic approach.

To test the appropriateness of a given database for specific research questions, we designed a checklist starting with the definition of an ideal database. This ideal database contains all relevant data on patients, providers and services. It is safe and accessible, input is always accurate, continuity is guaranteed and linkage with other information is easy. Of course no such database exists. Still these features are often taken for granted, but highly influenced by organizational processes in healthcare and prioritization. Starting with the characteristics of an ideal database, one can systematically list the required aspects for research goals and compare these with the available systems. This checklist is used to address important aspects of administrative database research and ethical issues. The increasing possibility to misuse sensitive data needs to be discussed by researchers, administrators, individuals and society. This checklist can also be valuable to others to design or interpret studies based on claims databases.

Benchmarking↗
PubMed2003

A comparison of adjustment methods to test the robustness of an STR DNA database comprised of 24 European populations.

An aim of the European Network of Forensic Science Institutes (ENFSI) is to produce a DNA database of second generation multiplex (SGM) STR profiles that is representative of the resident cosmopolitan populations. To achieve this, data were collected from 24 different populations. All of the data were combined to form one database of 5700 profiles from which allele proportions were calculated. The robustness of this combined European database was tested by estimating parameter d for every DNA profile, where d=log(10)(Pm(c)/Pm(E)) Pm(c) is the match probability of the profile calculated from its cognate database and Pm(E) is the match probability of the combined European database. Overall there was a small tendency for Pm(c)>Pm(E) primarily because of sampling bias. This bias was removed by the simple expediency of applying an adjustment factor to the calculation of Pm(E). These were selected from the Balding size bias correction, the Balding and Nichols Fst correction, a minimum allele proportion (between 0.01 and 0.02), an upper bound of a 95% confidence interval (CI) and a lower bound on the genotype match probability. It was demonstrated that a single European database is a feasible proposition. A combination of different adjustment methods can be used to ensure that the result is conservative relative to the cognate database, and their effect measured by parameter d.

Alleles↗
PubMed2003

A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases.

We present a new probability-based method for protein identification using tandem mass spectra and protein databases. The method employs a hypergeometric distribution to model frequencies of matches between fragment ions predicted for peptide sequences with a specific (M + H)+ value (at some mass tolerance) in a protein sequence database and an experimental tandem mass spectrum. The hypergeometric distribution constitutes null hypothesis-all peptide matches to a tandem mass spectrum are random. It is used to generate a score characterizing the randomness of a database sequence match to an experimental tandem mass spectrum and to determine the level of significance of the null hypothesis. For each tandem mass spectrum and database search, a peptide is identified that has the least probability of being a random match to the spectrum and the corresponding level of significance of the null hypothesis is determined. To check the validity of the hypergeometric model in describing fragment ion matches, we used chi2 test. The distribution of frequencies and corresponding hypergeometric probabilities are generated for each tandem mass spectrum. No proteolytic cleavage specificity is used to create the peptide sequences from the database. We do not use any empirical probabilities in this method. The scores generated by the hypergeometric model do not have a significant molecular weight bias and are reasonably independent of database size. The approach has been implemented in a database search algorithm, PEP_PROBE. By using a large set of tandem mass spectra derived from a set of peptides created by digestion of a collection of known proteins using four different proteases, a false positive rate of 5% is demonstrated.

Amino Acid Sequence↗
PubMed2004

Application of predictive QSAR models to database mining: identification and experimental validation of novel anticonvulsant compounds.

We have developed a drug discovery strategy that employs variable selection quantitative structure-activity relationship (QSAR) models for chemical database mining. The approach starts with the development of rigorously validated QSAR models obtained with the variable selection k nearest neighbor (kNN) method (or, in principle, with any other robust model-building technique). Model validation is based on several statistical criteria, including the randomization of the target property (Y-randomization), independent assessment of the training set model's predictive power using external test sets, and the establishment of the model's applicability domain. All successful models are employed in database mining concurrently; in each case, only variables selected as a result of model building (termed descriptor pharmacophore) are used in chemical similarity searches comparing active compounds of the training set (queries) with those in chemical databases. Specific biological activity (characteristic of the training set compounds) of external database entries found to be within a predefined similarity threshold of the training set molecules is predicted on the basis of the validated QSAR models using the applicability domain criteria. Compounds judged to have high predicted activities by all or the majority of all models are considered as consensus hits. We report on the application of this computational strategy for the first time for the discovery of anticonvulsant agents in the Maybridge and National Cancer Institute (NCI) databases containing ca. 250,000 compounds combined. Forty-eight anticonvulsant agents of the functionalized amino acid (FAA) series were used to build kNN variable selection QSAR models. The 10 best models were applied to mining chemical databases, and 22 compounds were selected as consensus hits. Nine compounds were synthesized and tested at the NIH Epilepsy Branch, Rockville, MD using the same biological test that was employed to assess the anticonvulsant activity of the training set compounds; of these nine, four were exact database hits and five were derived from the hits by minor chemical modifications. Seven of these nine compounds were confirmed to be active, indicating an exceptionally high hit rate. The approach described in this report can be used as a general rational drug discovery tool.

Amides↗
PubMed1997

Selecting optimally diverse compounds from structure databases: a validation study of two-dimensional and three-dimensional molecular descriptors.

The efficiency of the drug discovery process can be significantly improved using design techniques to maximize the diversity of structure databases or combinatorial libraries. Here, several physicochemical descriptors were investigated to quantify molecular diversity. Based on the 2D or 3D topological similarity of molecules, the relationship between physicochemical metrics and biological activity was studied to find valid descriptors. Several compounds were selected using those descriptors from a database containing diverse templates and 55 biological classes. It was evaluated whether the obtained subsets represent all biological properties and structural variations of the original database. In addition, hierarchical cluster analyses were used to group molecules from the parent database, which should have similar biological properties. Using various sets of structurally similar molecules, it was possible to derive quantitative measures for compound similarities in relation to biological properties. A similarity radius for 2D fingerprints and molecular steric fields was estimated; compounds within this radius of another molecule were shown to have comparable biological properties. This study demonstrates that 2D fingerprints alone or in combination with other metrics as the primary descriptor allow to handle global diversity. In addition, standard atom-pair descriptors or molecular steric fields can be used to correlate structural diversity with biological activity. Hence, the latter two descriptors can be classified as secondary descriptors useful for analog library design, while 2D fingerprints are applicable to design a general library for lead discovery. Based on these findings, an optimally diverse subset containing only 38% of the entire IC93 database was generated using 2D fingerprints. Here no structure is more similar than 0.85 to any other (Tanimoto coefficient), but all biological classes were selected. This reduction of redundancy led to a child database with the same physicochemical diversity space, which contains the same information as the original database.

Angiotensin-Converting Enzyme Inhibitors↗
PubMed2000

Do clinical databases render population-based cancer registers obsolete? The example of breast cancer in Denmark.

OBJECTIVE: Clinical databases have been invented to monitor treatment outcomes, therapies or diseases, often in great detail. The traditional population-based cancer registry has been invented to collect a minimum of information about all incident cancers. Do clinical databases render population-based cancer registers obsolete as sources of cancer cases for epidemiological study? METHODS: We compared the study base of first incident breast cancer cases in Denmark in 1978-1994 known from the national cancer register and from the national clinical database on breast cancer patients. The clinical database is used for monitoring protocoled treatment. RESULTS: Combining the two data sources we found 48,522 first primary breast cancers in Denmark 1978-1994. Of these, 37,640 were included in both data sources, 2151 were included only in the clinical database, and 8731 were included only in the cancer register. A major part of the difference between the two data sources was due to treatment-focused data collection in the clinical database, and a minor part due to differences in the registration of second primaries, date of diagnosis and invasiveness. CONCLUSIONS: Cancer incidence data are sensitive to registration procedures and definitions. Clinical cancer databases cannot generally replace the traditional cancer register as a reliable data source for incident cancer cases in a national population.

Adult↗
PubMed1999

An evaluation of EMBASE within the NHS: findings of the Database Access Project working partnership to extend the knowledge base of healthcare.

An earlier article in the Innovations on the Internet Series introduced the Database Access Project (DAPs) at Southmead Health Services NHS Trust, which piloted the introduction and use of EMBASE via the Internet and NHSnet. This follow-up article assesses the results of the Project, and reports on its findings. In particular, it considers the usefulness of EMBASE in terms of coverage and content for different groups of NHS users and aspects of take-up in terms of access arrangements and patterns of usage. It also considers the likely impact on the library and information service in terms of providing training and user support and meeting related demands, for example the acquisition of full-text articles as a result of increased levels of searching. The value of retaining access to EMBASE was recognized by the majority of those who participated in the Project, despite its acknowledged overlap with other databases. The coverage of the database was identified as being relevant by a majority of users; both its expanded European coverage and its coverage of drug-related and mental health literature were identified as important aspects. The project identified a clear preference for remote access to the database, although there was still a need to visit the library for retrieval of full text. Lack of time both for training and for actual database use, and lack of confidence in applying search skills and in appraising research were identified as key challenges to database searching. The authors highlight the special role of information professionals in providing training and support for NHS professionals in the acquisition of search skills and critical appraisal skills in order to encourage effective database use.

Computer User Training↗
PubMed2001

Coding diagnoses and procedures using a high-quality clinical database instead of a medical record review.

A discharge abstract must be completed for each hospitalization. The most time-consuming component of this task is a complete review of the doctors' progress notes to identify and code all diagnoses and procedures. We have developed a clinical database that creates hospital discharge summaries. To compare diagnostic and procedural coding from a clinical database vs. the standard chart review by health records analysts (HRA). All patients admitted and discharged from general medical and surgical services at a teaching hospital in Ontario, Canada. Diagnostic and procedural codes were identified by reviewing discharge summaries generated from a clinical database. Independently, codes were identified by hospital health records analysts using chart review alone. Codes were compared with a gold standard case review conducted by a health records analyst and a doctor. Coding accuracy (percentage of codes in gold standard review) and completeness (percentage of gold standard codes identified). The study included 124 patients (mean length of stay 5.5 days; 66.4% medical patients). The accuracy of the most responsible diagnosis was 68.5% and 62.9% for the database (D) and chart review (C), respectively (P = 0.18). Overall, the database significantly improved the accuracy (D = 78.9% vs. C = 74.5%; P = 0.02) and completeness (D = 63.9% vs. C = 36.7%; P < 0.0001) of diagnostic coding. Although completeness of procedural coding was similar (D = 5.4% vs. C = 64.2%; P = NS), accuracy decreased with the database (D = 70.3% vs. C = 92.2%; P < 0.0001). Mean resource intensity weightings calculated from the codes (D = 1.3 vs. C = 1.4; P = NS) were similar. Coding from a clinical database may circumvent the need for HRAs to review doctors' progress notes, while maintaining the quality of coding in the discharge abstract.

Database Management Systems↗
PubMed2006

SwePep, a database designed for endogenous peptides and mass spectrometry.

A new database, SwePep, specifically designed for endogenous peptides, has been constructed to significantly speed up the identification process from complex tissue samples utilizing mass spectrometry. In the identification process the experimental peptide masses are compared with the peptide masses stored in the database both with and without possible post-translational modifications. This intermediate identification step is fast and singles out peptides that are potential endogenous peptides and can later be confirmed with tandem mass spectrometry data. Successful applications of this methodology are presented. The SwePep database is a relational database developed using MySql and Java. The database contains 4180 annotated endogenous peptides from different tissues originating from 394 different species as well as 50 novel peptides from brain tissue identified in our laboratory. Information about the peptides, including mass, isoelectric point, sequence, and precursor protein, is also stored in the database. This new approach holds great potential for removing the bottleneck that occurs during the identification process in the field of peptidomics. The SwePep database is available to the public.

Animals↗