Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Database”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources
PubMed1991

Similarity graphing and enzyme-reaction database: methods to detect sequence regions of importance for recognition of chemical structures.

We developed a new method which searches sequence segments responsible for the recognition of a given chemical structure. These segments are detected as those locally conserved among a sequence to be analyzed (target sequence) and a set of sequences (reference sequences). Reference sequences are the sequences of functionally related proteins, ligands of which contain a common chemical substructure in their molecular structures. 'Similarity graphing' cuts target sequences into segments, aligns them with reference sequence pairwise, calculates the degree of similarity for each alignment, and shows graphically cumulative similarity values on target sequence. Any locally conserved regions, short or long in length and weak or strong in similarity, are detected at their optimal conditions by adjusting three parameters. The 'enzyme-reaction database' contains chemical structures and their related enzymes. When a chemical substructure is input into the database, sequences of the enzymes related to the input substructure are systematically searched from the NBRF sequence database and output as reference sequences. Examples of analysis using similarity graphing in combination with the enzyme-reaction database showed a great potentiality in the systematic analysis of the relationships between sequences and molecular recognitions for protein engineering.

Algorithms↗
PubMed1992

Influence of a computer database and problem exercises on students' knowledge of bacteriology.

This study compared the performances of students at the University of North Carolina at Chapel Hill School of Medicine who had access to sets of problem exercises and a computer database to support their learning of bacteriology with the performances of students at the University of Iowa College of Medicine who did not have such access. The study also examined the extent of a student's database use as a predictor of posttest performance. The students studied were randomly selected groups of 32-44 first-year students per year at each school; the study was conducted in three academic years (1988-1990) with some modifications in the intervention as the host environment evolved. The criterion measure was a posttest created from the same pool of problems used to generate the problem sets. The students at the intervention school scored significantly higher on the posttest in two of the three years, and overall. Also in two of the three years and overall, there was a significant relationship between the extent of a student's database use and his or her posttest score. Although the observed effects may have been due to other factors in this quasi-experimental design, the authors conclude that the use of problem sets and a computer database had a positive influence on the students' learning.

Bacteriology↗
PubMed1991

Gene maps and location databases.

A location database is defined in linear space by a vector of genetic and physical locations for each locus, which may be ordered by virtual sorting on composite location. This contrasts with an interval database defined in metric space, for which location must be inferred by list-processing from numbered intervals which are assigned different ordinals in different tables and overlap other intervals in many ways. A location database has been used for all well-studied experimental organisms. Principles for a human genome database may be derived from this experience.

Animals↗
PubMed2025

EucaMOD: a comprehensive multi-omics database for functional genomics research and molecular breeding of fast-growing eucalyptus trees.

Eucalyptus, one of the most widely planted plantation tree species globally, is primarily found in tropical and subtropical regions and contributes significantly to economic and social benefits. With advances in sequencing technologies, there is an increasing demand for the systematic analysis of multi-omics data among Eucalyptus species to enhance genetic breeding efforts. Although several early genomic databases have been established for eucalyptus, they have not been updated in a timely manner and lack recent multi-omics data, rendering them insufficient for current research needs. To address this gap, we developed the eucalyptus multi-omics database (EucaMOD, http://eucalyptusggd.net/eucamod), a comprehensive resource for cross-omics studies. In this study, we functionally annotated 45 eucalyptus genomes and structurally annotated 15, conducting comparative genomics and pan-proteomics analyses across all genomes. Additionally, we analyzed eucalyptus transcriptome, epigenome, and variome data through standardized workflows, enabling the in-depth mining and reanalysis of multi-omics datasets. EucaMOD is the most comprehensive multi-omics database for eucalyptus to date and includes data from 45 genomes (39 species), 870 mRNA-seq samples, 17 miRNA-seq samples, 52 epigenomic datasets (histone modifications and transcription factor binding), and genetic variation data from 1219 samples. To support functional genomics and molecular breeding research, the database is organized into the following 11 modules: Home, Species, Genomics, Comparative genomics, Pan-proteomics, Transcriptomics, Epigenetics, Variomics, Tools, Download, and Help. EucaMOD also offers online analysis tools for data mining, providing free public services to aid eucalyptus gene function and genetic engineering studies.

Eucalyptus↗
PubMed1991

Computer-assisted instruction in otolaryngology: the use of a database for examination review.

A database of questions and answers has been developed to assist residents in reviewing current topics in otolaryngology-head and neck surgery. Each question/item has an associated answer, general category, specific category, and reference that allows cross-referencing on the computer system. The user can search the database for categories of interest and obtain a specific subset of questions. This allows an efficient means of knowledge acquisition and review for Board examinations. Additional data entry is also facilitated to expand the database as desired. Currently there are more than 2300 items in the database.

Computer-Assisted Instruction↗
PubMed1991

The need for a control animal pathology database: an international survey.

1. The sensitivity of long-term toxicity tests is impaired due to the 'background noise' of spontaneous lesions which are unrelated to treatment. 2. The need for a comprehensive source of computerized information concerning the occurrence and incidence of spontaneous lesions in control animals has been highlighted by initiatives in Europe and the USA. It is, however, essential to identify the potential users, and the type of information required for such a database to be of value. 3. This information has been acquired following an international survey of the pharmaceutical industry in Europe, Japan and the USA, including responses from 48 toxicologists and toxicopathologists representing 38 company groups. 4. Thirty-eight respondents indicated that they would use a historical control database that was regularly updated with the majority of respondents suggesting that they currently use external sources (Breeder's data, the literature, other companies) occasionally to acquire information on control animal pathology data. 5. The majority (94%) of the respondents indicated that a control animal database should contain information on both neoplastic and non-neoplastic lesions for use in evaluating long-term studies, in particular carcinogenicity studies. 6. The survey confirms the need for a historical control animal pathology database wider then those currently available.

Animals↗
PubMed2026

Worldwide Innovative Network Consortium: Building a Common Global Cancer Database.

This review shares the ongoing work of the global Worldwide Innovative Network (WIN) Consortium for Precision Medicine to synthesize emerging cancer treatment data and to define the requirements for a common global cancer database that can truly support precision oncology. We performed a narrative review of emerging cancer treatment data, molecular profiling technologies, and existing clinicogenomic databases, focusing on how tumors are characterized, how subgroups are defined, and how demographic, lifestyle, and environmental factors are captured. The growth in molecular profiling technologies and the development of new targeted therapies are transforming cancer care. Tumors, regardless of tissue origin, are increasingly defined as composites of multiple, often rare, subgroups, each with distinct biology and likely response to specific therapies, based on multidimensional profiling of the tumor and its microenvironment. The solution lies in building vast databases that capture racial and ethnic diversity, reflected in genomic data, as well as diet and lifestyle factors that may have epigenetic impact on gene expression and post-translational modifications. A truly inclusive and informative data set must reflect global diversity, and there are multiple examples of demography-dependent differences in genomic signals. With members caring for and studying patients with cancer across five continents, WIN is actively exploring pathways to create a global cancer database, rich in clinical and molecular detail, granular enough for precise analysis, and large enough to power artificial intelligence-driven insights, provided appropriate data quality, validation, and governance frameworks are in place. This review surveys the current landscape and outlines practical paths forward to achieve this goal.

Humans↗
PubMed1991

Predicting mammalian mutagenesis by submammalian assays: an application of database GEN.

A database containing qualitative information on the genotoxic activity of about 3000 chemicals is described. The initial aim for the construction of the database was to develop an instrument for comparing the performance of different genotoxicity assay systems. One application of the database is the prediction of expected results in any genotoxicity assay for chemicals that were tested in a small number of genotoxicity assays. The Bayesian prediction is calculated based on the sensitivities and specificities between any predictive test and the target test for which the prediction is to be determined. The predictivity of the system for in vivo mammalian assays is at present (with the exception of the micronucleus assay and the in vivo sister chromatid exchanges) limited, in particular because of the limited number of chemicals tested in the expensive in vivo assays and, in addition, due to the lack of sufficient information on negative compounds. A continued updating of the database will possibly help to overcome some of the present difficulties.

Animals↗
PubMedDate not supplied

An electrocardiogram database incorporated into the hospital information system.

A database system was developed for storing and retrieving electrocardiogram (ECG) interpretations made by the Bonner program. One ECG record consists of the patient identification information, measurement matrix, and interpretive statements made by the program and by the reviewing cardiologist. The logical structure of the database is 3-level hierarchy. An ECG record is automatically inserted into the database when an ECG signal is analysed by the program. Stored ECG records can easily be retrieved using any parameter and qualifier for review, research and education. The physician can gather statistics on the parameters and qualifiers of the extracted ECG records using statistical program packages (BDMP, SCSS) and a decision support system (AS). Since the database management system is DL/I, the newly developed system can be transferred to various computers, and the relationships between the ECG findings and clinical records stored in the DL/I form can easily be studied.

Database Management Systems↗
PubMed1992

Combining new technologies for effective collection development: a bibliometric study using CD-ROM and a database management program.

Librarians have used bibliometrics for many years to assess collections and to provide data for making selection and deselection decisions. With the advent of new technology--specifically, CD-ROM databases and reprint file database management programs--new cost-effective procedures can be developed. This paper describes a recent multidisciplinary study conducted by two library faculty members and one allied health faculty member to test a bibliometric method that used the MEDLINE and CINAHL databases on CD-ROM and the Papyrus database management program to produce a new collection development methodology.

Bibliometrics↗
PubMed1991

Estimating frequency of disease findings from combined hospital databases: a UMLS project.

Merging data from the Salt Lake VA hospital database and the LDS hospital HELP system into a UMLS sponsored unified patient database has demonstrated that distribution of variables within a disease is hospital independent. Although disease prevalence is clearly not the same among hospitals, analysis of data within a disease group across hospitals can be done using such a merged database. This unified patient database would allow study of unusual diseases not possible using data from a single institution.

Databases, Factual↗
PubMed1991

AuthorBase: a database of authoring systems software.

A working prototype database of authoring system software was developed as part of a study of authoring software conducted by the National Library of Medicine. The database and development issues ranging from the scope of the database to what information to document are described. The protype demonstrates that records of reasonable integrity can be derived from vendor supplied information as long as users understand the database is only an initial starting point in searching for authoring software and a resource for becoming generally familiar with the technology.

Authorship↗
PubMed1990

Key health indicators database.

A new database developed by the Canadian Centre for Health Information (CCHI) contains 40 key health indicators and lets users select a range of disaggregations, categories and variables. The database can be accessed through CANSIM, Statistics Canada's electronic database and retrieval system, or through a package for personal computers. This package includes the database on diskettes, as well as software for retrieving and manipulating data and for producing graphics. A data dictionary, a user's guide and tables and graphs that highlight aspects of each indicator are also included.

Canada↗
PubMed1990

NRL-3D: a sequence-structure database derived from the protein data bank (PDB) and searchable within the PIR environment.

The protein identification resource (PIR) and the Brookhaven National Laboratory protein data bank (PDB) are well-known databases for primary sequences and three-dimensional structures of proteins, respectively. Lesk et al, have compared the primary sequences in these two databases and concluded that the sequences in them are not redundant. Moreover, PIR programs can not be used directly on PDB files to access primary sequences because the FORMATS of these two data bases are different. We have developed a sequence-structure database, called NRL-3D, from the sequences, chain identification and the residue numbers of proteins in the PDB. This new database is designed such that it can be used in conjunction with PIR programs to search and extract sequences of interest and the corresponding three-dimensional coordinates from the structures in PDB.

Amino Acid Sequence↗
PubMedDate not supplied

Development of a Database Management System for an obstetrics unit.

This article discusses the use of computer technology in expediting and simplifying the retrieval of data generated from clinical practice. The article describes the collaboration between academic faculty and nurse clinicians in developing a computerized database to report birth statistics incurred by a busy obstetrical unit. A secondary purpose of the article is to assist the reader in understanding the importance of planning the content to be entered into the database and to become familiar with the basics of developing a database that could be used to sort and retrieve data. Facilitators and barriers to the development of a database management system in clinical practice are also discussed.

Database Management Systems↗
PubMed1988

Design of clinical database management systems and associated software to facilitate medical statistical research.

Clinical databases are growing rapidly. The clinical database is heavily used for medical research in many settings. This paper discusses design features for medical databases that facilitate their use for research. The database management system should allow complex data structures, have a syntax-facilitating collection of longitudinal data, interface with major statistical software packages, allow an extensive data dictionary, conveniently merge files, facilitate archival documentation, have an associated data entry system that allows complex logical checking, and have coordinated mainframe and microcomputer software.

Biometry↗
PubMedDate not supplied

A research database for improved data management and analysis in longitudinal studies.

We developed a research database for a five-year prospective investigation of the medical, social, and developmental correlates of chronic lung disease during the first three years of life. We used the Ingres database management system and the Statit statistical software package. The database includes records containing 1300 variables each, the results of 35 psychological tests, each repeated five times (providing longitudinal data on the child, the parents, and behavioral interactions), both raw and calculated variables, and both missing and deferred values. The four-layer menu-driven user interface incorporates automatic activation of complex functions to handle data verification, missing and deferred values, static and dynamic backup, determination of calculated values, display of database status, reports, bulk data extraction, and statistical analysis.

Bronchopulmonary Dysplasia↗
PubMed2026

circASbase: A Comprehensive Database of Alternative Splicing Events in circRNAs.

Although extensive evidence has underscored the critical role of alternative splicing (AS) in generating mature circular RNA (circRNA) isoforms and augmenting their functional diversity, a significant gap remains in the availability of specialized databases housing circRNA AS events. To bridge this gap, we develop circASbase, a pioneering and comprehensive database that catalogs 452,129 AS events in 884,047 full-length circRNAs from 581 samples across 13 species, and provides rich annotations to facilitate understanding the splicing regulation of circRNA. Our findings reveal substantial differences between circRNAs and linear transcripts regarding the distribution and occurrence of AS events, highlighting the unique regulatory landscape of circRNAs. These special splicing events result in functional differences of circRNAs by affecting internal ribosome entry sites, N6-methyladenosine sites, open reading frames, protein features, microRNA targets, and more. In summary, circASbase not only meets the urgent need of the research community for data repositories, but also represents a significant advancement in our understanding of circRNA biology. With its user-friendly interfaces and web-based visualization tools, circASbase is poised to become an indispensable resource for researchers exploring the regulatory mechanisms and functional roles of AS events in circRNAs. This database will continuously drive new insights and discoveries in the field, setting the stage for further advancements in circRNA research. circASbase is freely available at http://reprod.njmu.edu.cn/cgi-bin/circASbase/.

Alternative Splicing↗