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PubMed1995

Exploration and virtual experimentation in a local neuroscience database.

Work is currently being done by a number of groups to investigate the possibility of creating one or more neuroscience databases. These databases could provide: (1) a means for conveying complete descriptions of experiments; (2) a platform for virtual experiments; (3) and an interface where modeling and experimental results could be exchanged. This paper describes work towards creating a local database with these capabilities by creating a set of experimental neurophysiology software tools that are tied to a database of experiment descriptions via external scripting mechanisms. These tools provide a means of exploring results and data that can lead to insights into the data that suggest new avenues of research. Because the scriptability of the tools allows for automation of re-analysis of the data, virtual experiments for testing new hypotheses over large datasets becomes possible. Such virtual experiments are particularly relevant to computational neuroscience, as they allow hypotheses generated by models to be immediately tested without further collection of experimental data.

Animals↗
PubMed1991

The PDQ (Physician Data Query), the cancer database, in oncological clinical practice.

The above illustrates the fact that a physician interested in consulting the PDQ database must dedicate a certain amount of time to an analytical review of the database. It is difficult to determine how much time is required to acquire a sufficient level of control because there are many variables affecting the learning time: experience in using computerized systems, cultural background, personal inclination, etc. However, a certain amount of caution and humility should be exercised whenever a physician approaches a database of this type for the first time, in order to avoid the mistake of dangerously underestimating the nature of the problem. On the other hand, the physician's specific competence and professionalism will not be questioned at all, since they are fundamental to obtain productive search results. If, indeed, the above discussion focussed heavily on the most closely documental aspect of the problem, it should not be forgotten that the contents of the database can be fully understood only by experts who are used to encountering certain terms and procedures on a daily basis. In fact, when a physician turns to a documentation center for a PDQ research, the physician's assistance is always requested in order pair clinical and documental competence. It is this second skill that the physician must acquire to become totally independent.

Databases, Factual↗
PubMed1995

ATSDR's information databases to support human health risk assessment of hazardous substances. Agency for Toxic Substances and Disease Registry.

The American public, like persons in many other nations, is concerned about the potential adverse impacts of uncontrolled hazardous wastes. The concerns are often predicated on the fear that adverse health effects will occur because of releases of hazardous substances into community environments. To respond to these concerns, government agencies and private sector organizations must rely on credible, accessible, up-to-date information databases. These databases should be relevant to the needs of the people who respond to uncontrolled releases of hazardous substances. Of particular importance are databases that profile the toxicity of hazardous substances and other information useful to physicians and other health care providers. This paper describes how the federal Agency for Toxic Substances and Diseases Registry (ATSDR) has developed several toxicologic and human health information databases under mandates in the Superfund statute for responding to the public's concerns about hazardous substances.

Databases, Factual↗
PubMed1989

Review of Papyrus bibliographic database software.

Papyrus is an inexpensive bibliographic database which provides some features not found in other similar packages. Its flexibility in handling references of many types and formats, its capacity for integration with manuscripts prepared with word processors, its capacity for importing references from national databases and its ability to perform microcosmic literature searches are attractive features. Because Papyrus has tackled a complex task, mastery of the intricacies of the program may present a substantial challenge to novice computer users. Although the manipulation of an existing customized bibliographic database would seem to be attractive for any researcher or author who prepares manuscripts for publication, the optimal use of the program also requires an extensive commitment of time and labor for the initial entry of all pertinent references into the database. While this could be accomplished gradually in conjunction with the preparation of individual manuscripts, the creation of a complete file of references could require hundreds of hours of labor. Individual authors, as well as larger research groups, should be prepared for this type of commitment before acquiring the Papyrus system.

Bibliographies as Topic↗
PubMed2025

An adjuvant database for preclinical evaluation of vaccines and immunotherapeutics.

Adjuvants are immunostimulators used to enhance vaccine efficacy against infectious diseases. However, current methods for evaluating their efficacy and safety are limited, hindering large-scale screening. To address this, we developed a prototype Adjuvant Database (ADB) containing transcriptome data, generated using the same protocols as the widely used Open TG-GATEs (OTG) toxicogenomics database, covering 25 adjuvants across multiple species, organs, time points, and doses. This enabled cross-database integration of ADB and OTG. Transcriptomic patterns successfully distinguished each adjuvant regardless of organs or species. Using both databases, we built machine learning models to predict adjuvanticity and hepatotoxicity. Notably, we identified colchicine's adjuvant activity and FK565's liver toxicity through data-driven analysis. Overall, ADB combined with OTG offers a framework for transcriptomics-based, data-driven screening of adjuvant candidates.

Animals↗
PubMed2004

Generation of digital time database from paper ECG records and Fourier transform-based analysis for disease identification.

ECG signals recorded on paper are transferred to the digital time database with the help of an automated data extraction system developed here. A flatbed scanner is used to form an image database of each 12-lead ECG signal. Those images are then fed into a Pentium PC having a system to extract pixel-to-pixel co-ordinate information to form a raw database with the help of some image processing techniques. These raw data are then ported to the regeneration domain of the system to check the captured pattern with the original wave shape. The sampling period of each ECG signal is computed after detection of QRS complex. Finally, discrete Fourier transform of the generated database is performed to observe the frequency response properties of every ECG signal. Some interesting amplitude properties of monopolar chest lead V4 and V6 are noticed which are stated.

Databases as Topic↗
PubMed2004

Novel biocatalysis by database mining.

Broad-based adoption of biocatalytic methods will require widely available database tools, analogous to previous efforts compiling information for the facilitation of chemical synthesis. The analog to chemical reagents are enzymes. The analog to chemical synthetic routes are metabolic pathways. The free on-line database BRENDA exemplifies efforts to compile relevant information on enzymes for biocatalytic purposes. Likewise, the University of Minnesota Biocatalysis/Biodegradation Database focuses on novel enzymes and metabolic pathways useful in environmental and industrial biotechnology. The development of biocatalytic protocols will be facilitated by the increasing availability of well-curated database information on enzymatic enantioselectivity and capabilities for transforming disparate chemical functional groups.

Catalysis↗
PubMed2005

An attempt at data verification in the EACTS Congenital Database.

OBJECTIVE: The multi-national and multi-institutional collection of data on outcomes in Congenital Heart Surgery (CHS) provides the possibility of analysis of results of treatment and may result in further improvement of the quality of care. The verification of data as far as the completeness and accuracy is necessary to give confidence to all sides--the patients, centers and regulatory authorities. The source data verification (SDV), although difficult, appears possible even in such a large-scale database. METHODS: Out of 5.274 patients and 5.612 procedures data of 2003, collected in the database, 1.703 (32.3%) and 1.895 (33.8%), respectively, have been verified at five sites on following fields: IPPV time, date of birth, date of admission, date of surgery, date of discharge/mortality, body weight, case category, CPB time, AoX time, Circulatory arrest time. SDV was performed at five sites by two database officers using the sources of information different to the local copy of the database (patients' files, operation notes, perfusion charts, OR Books). Verification was performed between June 1st and July 31st 2004. Statistical analysis was performed using R-project software, ver. 2.0.0. and Welch's t-test for comparison of continuous variables. P-value >0.05 was used as statistically significant difference between groups. RESULTS: Pre- and post-verification mortalities in all groups showed no significant differences although seven deaths out of 68 (10.27%) were missed. None of the other verified fields showed significant differences after verification. CONCLUSIONS: Source Data Verification showed no statistically significant differences between verified and non-verified data on 30 days mortality, LOS, age, body weight, CPB time, AoX and Circulatory arrest time. IPPV time was not available in 58.6% procedures.

Data Collection↗
PubMed2005

CysMap and CysJoin: database and tools for protein disulphides localisation.

We have developed a computer program able to make user-customised databases derived from the public PIR non-redundant reference protein database. When the database of interest has been created, the user will generate the map of all the possible linear peptides containing one and two cysteines for each protein and combine them to calculate the mass of all the possible clusters of linear peptides linked by a disulphide bridge with a cysteine pair. It is also possible to create selected maps corresponding to peptides formed by the action of specific proteases. In this way, mass spectrometric data obtained from the hydrolysis of proteins of unknown sequence can be related to that contained in the database for quick disulphide assignment and protein identification. To confirm signal attribution, the program will also furnish the expected mass of cluster peptides after performing a cycle of Edman degradation. The utility of the program is discussed and examples of application are given.

Amino Acid Sequence↗
PubMed2005

Forensic genetic analysis of mitochondrial DNA hypervariable region I/II sequences: an expanded Korean population database.

We have analyzed variation of the mitochondrial DNA (mtDNA) hypervariable segments I and II (HVS-I and HVS-II) in 185 randomly chosen individuals from Korea to provide an expanded and reliable Korean database. Combined sequence comparison of HVS-I and HVS-II led to the identification of 167 different haplotypes characterized by 154 variable sites. One hundred and fifty-one of the haplotypes were individual-specific, 14 were found in two individuals and 2 were found in three individuals. A pairwise comparison of the 185 HVS-I/II sequences found an average of 10.11 +/- 4.63 differences between individuals. The random match probability and gene diversity for the combined hypervariable regions were estimated at 0.66% and 0.9988, respectively. Analyzing the expanded database including three previously reported data sets and the present data using haplogroup-based comparisons and comparison with closely related sequences allowed errors to be detected and eliminated, thus considerably improving data quality. Sample division comparisons based on PhiST genetic distance measures revealed no significant population differentiation in the distribution of mtDNA sequence variations between the present data set and a database in The Scientific Working Group on DNA Analysis Methods (SWGDAM), but did indicate differences from other sets of data. Based on the results of mtDNA profiles, almost all of the mtDNA types studied here could be classified into subsets of haplogroups common in east Asia, and show that the Koreans possess lineages from both the southern and the northern haplogroup complexes of east Asian populations. The new data, combined with other mtDNA sequences, demonstrate how useful comparison with closely related mtDNA sequences can be for improving database quality, as well as providing haplotype information for forensic and population genetic analyses in the Korean population.

Asian People↗
PubMed2006

Penaeus monodon gene discovery project: the generation of an EST collection and establishment of a database.

A large-scale expressed sequence tag (EST) sequencing project was undertaken for the purpose of gene discovery in the black tiger shrimp Penaeus monodon. Initially, 15 cDNA libraries were constructed from different tissues (eyestalk, hepatopancrease, haematopoietic tissue, haemocyte, lymphoid organ, and ovary) of shrimp, reared under normal or stress conditions, to identify tissue-specific genes and genes responding to infection and heat stress. A total of 10,100 clones were analyzed by single-pass sequencing from the 5' end. Clustering and assembling of these ESTs resulted in a total of 4845 unique sequences with 917 overlapping contigs and 3928 singletons. The redundancy of each cDNA library ranged from 13.4% to 61.3% with an overall redundancy of 61.1%. About half of these ESTs (2365 clones, 48.8%) showed significant homology (BLASTX, e-values <10(-4)) to known genes. A high proportion of P. monodon ESTs was most similar to the predicted protein sequences from various organisms, e.g. Homo sapiens (9%), Mus musculus (7%), Drosophila (6%), Gallus sp.(6%), and Anopheles (5%). Only 6% showed the highest similarity to other known genes from shrimp due to the limited sequence entries of the species in the public database. Several tissue-specific transcripts were identified as well as the candidate genes that may be implicated in the immune response. In addition, bioinformatic mining of microsatellites from the P. monodon ESTs identified 997 unique microsatellite containing ESTs in which 74 loci resided within the genes of known functions. Consequently, the P. monodon EST database was established. The EST sequence data and the BLAST results were stored and made available through a web-accessible database (). This EST database provides a useful resource for gene identification and functional genomic studies of shrimp.

Animals↗
PubMed2025

Unique signatures of highly constrained genes across publicly available genomic databases.

PURPOSE: Publicly available genomic databases are critical in understanding human genetic variation. They also provide unique insights into patterns of genetic constraints and their relationship with human disease. METHODS: We utilized one of the largest publicly available databases, Genome Aggregate Database, to determine genes that are highly constrained for only loss-of-function, only missense, and both loss-of-function/missense variants. We identified their unique signatures and explored their causal relationship with human diseases. Those genes were also evaluated for chromosomal location, tissue-level expression, Gene Ontology analysis, and gene family categorization using multiple publicly available databases. RESULTS: We identified unique patterns of inheritance, protein size, and enrichment in distinct molecular pathways for those constrained genes associated with human disease. In addition, we identified genes that are currently not known to cause human disease, which may be excellent gene discovery candidates. CONCLUSION: We elucidate biological pathways of highly constrained genes that expand our understanding of critical cellular proteins. The findings can also advance research in rare diseases.

Humans↗
PubMed2005

PSSARD: protein sequence-structure analysis relational database.

We have implemented a relational database comprising a representative dataset of amino acid sequences and their associated secondary structure. The representative amino acid sequences were selected according to the PDB_SELECT program by choosing proteins corresponding to protein crystal structure data deposited in the protein data bank that share less than 25% overall pair-wise sequence identity. The secondary structure was extracted from the protein data bank website. The information content in the database includes the protein description, PDB code, crystal structure resolution, total number of amino acid residues in the protein chain, amino acid sequence, secondary structure conformation and its summary. The database is freely accessible from the website mentioned below and is useful to query on any of the above fields. The database is particularly useful to quickly retrieve amino acid sequences that are compatible to any super-secondary structure conformation from several proteins simultaneously.

Amino Acid Sequence↗
PubMed2006

A protein database constructed from low-coverage genomic sequence of Bacillus megaterium and its use for accelerated proteomic analysis.

Peptide mass fingerprint (PMF) matching is a high-throughput method used for protein spot identification in connection with two-dimensional gel electrophoresis (2DE). However, the success of PMF matching largely depends on whether the proteins to be identified exist in the database searched. Consequently, it is often necessary to apply other more sophisticated but also time-consuming technologies to generate sequence-tags for definitive protein identification. On the other hand, modern sequencing technologies are generating a large quantity of DNA sequences, first in unfinished form or with low genome coverage due to the time-consuming and thus limiting steps of finishing and annotation. We recently started to sequence the genome of Bacillus megaterium DSM 319, a bacterium of industrial interest. In this study, we demonstrate that a protein database generated from merely three-fold coverage, unfinished genomic sequences of this bacterium allows a fast and reliable protein spot identification solely based on PMF from high-throughput MALDI-TOF MS analysis. We further show that the strain-specific protein database from low coverage genomic sequence greatly outperforms the commonly used cross-species databases constructed from 13 completely sequenced Bacillus strains for protein spot identification via PMF.

Algorithms↗
PubMed2005

Local and national electronic databases in Norway demonstrate a varying degree of validity.

OBJECTIVE: The aim of the present study was to examine the validity of local and national electronic databases using medical records as gold Standard. STUDY DESIGN AND SETTING: All hospital admissions with ICD 9-code 820.X (hip fracture) in a 1-year period were identified in the electronic discharge registers of the hospitals in Oslo and in the national electronic database (The Norwegian Patient Register). Medical records for all patients identified by the discharge registers and the logbooks of the operating theater of the hospitals were retrieved, and the diagnosis was verified. RESULTS: Compared with the total number of fractures confirmed in medical records, the electronic discharge register of one of the hospitals underestimated the number of fractures by 46%, whereas the two other overestimated the number by 17% and 19%. For the national electronic database, an overall overestimation of 19% was found. CONCLUSION: The present findings question the validity of electronic databases and thus have implications for epidemiologic studies.

Aged↗
PubMed2005

A review of uses of health care utilization databases for epidemiologic research on therapeutics.

OBJECTIVE: Large health care utilization databases are frequently used in variety of settings to study the use and outcomes of therapeutics. Their size allows the study of infrequent events, their representativeness of routine clinical care makes it possible to study real-world effectiveness and utilization patterns, and their availability at relatively low cost without long delays makes them accessible to many researchers. However, concerns about database studies include data validity, lack of detailed clinical information, and a limited ability to control confounding. STUDY DESIGN AND SETTING: We consider the strengths, limitations, and appropriate applications of health care utilization databases in epidemiology and health services research, with particular reference to the study of medications. CONCLUSION: Progress has been made on many methodologic issues related to the use of health care utilization databases in recent years, but important areas persist and merit scrutiny.

Bias↗
PubMed2005

Searching one or two databases was insufficient for meta-analysis of observational studies.

OBJECTIVE: To address methodologic issues in searching for observational studies by presenting database search methods and results. STUDY DESIGN AND SETTING: Results of two literature searches for publications reporting on observational studies of alcohol consumption and the risk of breast cancer and large bowel cancer were compared, to evaluate the sensitivity of various bibliographic databases and search strategies, including hand-searching reviews and meta-analyses. RESULTS: The target sensitivity of 90% of publications in the breast cancer search was achieved by starting with Medline, then adding Biosis, Embase, and SCI EXPANDED-SSCI, which provided a total of 72 (91%) of the 79 relevant publications. To reach a similar 89% sensitivity for large bowel cancer, at least Biosis, Dissertation Abstracts Online, Embase, ETOH, and Medline had to be searched, with the addition of hand search of reviews and meta-analyses. CONCLUSION: Limiting a search to one or two databases when conducting meta-analyses of observational studies will not provide a thorough summary of the existing literature. The findings support recommendations to implement a comprehensive search of electronic databases and the reference lists of recent review articles and meta-analyses.

Alcohol Drinking↗
PubMed2005

A systematic review of the Charlson comorbidity index using Canadian administrative databases: a perspective on risk adjustment in critical care research.

The Charlson index is commonly used for risk adjustment in critical care health services research. However, the literature supporting this methodology has not been thoroughly explored. We systematically reviewed the literature related to administrative database adaptations of the Charlson index. Our review has 3 major findings. First, 2 studies compared Canadian administrative databases with chart review for obtaining Charlson comorbidity data. Agreement between the database and chart review was substantial (kappa > 0.70), and mortality prediction did not differ. Second, 5 database adaptations were identified with the Deyo and Dartmouth-Manitoba adaptations being most popular. Three studies directly compared these 2 popular adaptations and demonstrated substantial agreement (kappa > 0.70) and similar predictive ability for mortality. Third, one study validated the Charlson index for critically ill patients but demonstrated that APACHE (Acute Physiology and Chronic Health Evaluation) II better discriminates inhospital mortality (area under curve 0.67 vs 0.87). Time and cost barriers prevent widespread use of physiology-based risk adjustment in population-based research. The decreased predictive ability of the Charlson index must be weighed against the advantages of using this instrument for population-based research. Future research should focus on updating the Charlson index for recent changes in the prognosis of comorbid diseases and introduction of International Statistical Classification of Diseases, 10th Revision coding of discharge abstracts.

Canada↗