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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↗
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↗
PubMed1992

The Human Communication Research Centre dialogue database.

The HCRC dialogue database consists of over 700 transcribed and coded dialogues from pairs of speakers aged from seven to fourteen. The speakers are recorded while tackling co-operative problem-solving tasks and the same pairs of speakers are recorded over two years tackling 10 different versions of our two tasks. In addition there are over 200 dialogues recorded between pairs of undergraduate speakers engaged on versions of the same tasks. Access to the database, and to its accompanying custom-built search software, is available electronically over the JANET system by contacting liz@psy.glasgow.ac.uk, from whom further information about the database and a user's guide to the database can be obtained.

Adolescent↗
PubMed1991

The PHARMSEARCH database.

PHARMSEARCH, a database produced by the French Patent and Trademark Office (INPI), covers pharmaceutical patents issued by the Europeans, French, and United States patent offices from November 1986 onward. PHARMSEARCH is composed of MPHARM, a structure file searchable using Markush DARC software, and PHARM, the companion bibliographic file. Markush structures claimed in the patent documents are entered into the database as variable generic structures. Specific structures are also included in the database, when they are not part of a Markush structure in the patent document. Chemical index terms describe all moieties of the structure. Indexing also describes the therapeutic activities and preparation processes for the compounds. The indexing policies used in the production of this database are described.

Abstracting and Indexing↗
PubMed1991

A database of lipid phase transition temperatures and enthalpy changes.

The systematic study of the mesomorphic phase properties of synthetic and biologically derived lipids began some 30 years ago. In the past decade, interest in this area has grown enormously. As a result, there exists a wealth of information on lipid phase behavior, but unfortunately, these data have, until now, been scattered throughout the literature in a variety of books, proceedings, and journals. The data have recently been compiled in a centralized database with a view to providing ready access to the same and to the appropriate literature. The compilation facilitates review of what has thus far been accomplished and highlights what remains to be done in this active research area. As such, it represents a convenient summary of the existing data which, when evaluated, will enable us to identify where deficits exist in the data, to reveal the fundamental physicochemical principles upon which lipid phase behavior is based, and to understand more completely lipid phase relations in biological, reconstituted, and formulated systems. The compilation consists of a tabulation of all known mesomorphic and polymorphic phase transition temperatures and enthalpy changes for synthetic and biologically derived lipids in the dry and in the partially and fully hydrated states. Also included is the effect on these thermodynamic values of pH, and of salt and metal ion concentration and other additives such as proteins, drugs, etc. The methods used in making the measurements and the experimental conditions are reported. Bibliographic information includes complete literature referencing and list of authors. As of this writing, the database is current through June 1990 and contains 9500 records. Each record contains 28 fields. Here, we describe how the database originated, its scope and contents, data abstraction procedures, and issues relating to mesophase and lipid nomenclature, data analysis, and evaluation, and database maintenance and distribution.

Databases, Factual↗
PubMedDate not supplied

Role of exposure databases in epidemiology.

At present, exposure databases record data primarily for regulatory purposes; they have not focused on serving the needs of epidemiologists or public health. However, the modification of exposure databases could facilitate their use in epidemiology. Characteristics necessary to enhance the use of all databases include easy access by users; documentation of methods, sampling bias, error, and inconsistences; widespread coverage in time and space; and methods and measures for estimating exposure of individuals as well as populations. Also needed are exposure scenarios and models to estimate exposures for geographic areas and time intervals not currently sampled. Multidisciplinary teams are needed to examine current databases, to review strategies for improving data collection, and to suggest and help implement appropriate changes. A long-term goal is to develop and validate data from exposure scenarios and models using data on the relationship of exposure to doses measured in humans.

Databases, Factual↗
PubMed1992

The European ST-T database: standard for evaluating systems for the analysis of ST-T changes in ambulatory electrocardiography.

The project for the development of the European ST-T annotated Database originated from a 'Concerted Action' on Ambulatory Monitoring, set up by the European Community in 1985. The goal was to prototype an ECG database for assessing the quality of ambulatory ECG monitoring (AECG) systems. After the 'concerted action', the development of the full database was coordinated by the Institute of Clinical Physiology of the National Research Council (CNR) in Pisa and the Thoraxcenter of Erasmus University in Rotterdam. Thirteen research groups from eight countries provided AECG tapes and annotated beat by beat the selected 2-channel records, each 2 h in duration. ST segment (ST) and T-wave (T) changes were identified and their onset, offset and peak beats annotated in addition to QRSs, beat types, rhythm and signal quality changes. In 1989, the European Society of Cardiology sponsored the remainder of the project. Recently the 90 records were completed and stored on CD-ROM. The records include 372 ST and 423 T changes. In cooperation with the Biomedical Engineering Centre of MIT (developers of the MIT-BIH arrhythmia database), the annotation scheme was revised to be consistent with both MIT-BIH and American Heart Association formats.

Algorithms↗
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↗