Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Catalogs as Topic”

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 1,405 records · Page 78Linked to original sources
PubMed2001

Guidelines for genetic nomenclature and community governance for the model legume Medicago truncatula.

At the 2nd Medicago meeting (a satellite of the 1999 IS-MPMI meeting in Amsterdam), investigators perceived a need for standardization of genetic nomenclature in Medicago truncatula, due to the rapid growth of research on this species in the past few years. Establishment of such standards grew out of discussions begun at this meeting and continued electronically throughout the M. truncatula community. The proposed standards presented here are the consensus results of those discussions. In addition to standards for gene nomenclature, a method for community governance and a website for cataloging gene names and submitting new ones are presented. The purpose of implementing these guidelines is to help maintain consistency in the literature, to avoid redundancy, to contribute to the accuracy of databases, and, in general, to aid the international collaborations that have made M. truncatula a model system for legume biology.

Genes, Bacterial↗
PubMed1978

Hospital-based patient education programs and the role of the hospital librarian.

This paper examines current advances in hospital-based patient education, and delineates the role of the hospital librarian in these programs. Recently, programs of planned patient education have been recognized by health care personnel and the public as being an integral part of health care delivery. Various key elements, including legislative action, the advent of audiovisual technology, and rising health care costs have contributed to the development of patient education programs in hospitals. As responsible members of the hospital organization, hospital librarians should contribute their expertise to patient education programs. They are uniquely trained with skills in providing information on other health education programs; in assembling, cataloging, and managing collections of patient education materials; and in providing documentation of their use. In order to demonstrate the full range of their skills and to contribute to patient care, education, and research, hospital librarians should actively participate in programs of planned patient education.

Cost-Benefit Analysis↗
PubMed2002

Tobacco harm reduction: conceptual structure and nomenclature for analysis and research.

The goal of tobacco control has always been to reduce death and disease due to tobacco use. Recent discussions have broadened the concept of tobacco control beyond cessation and prevention to include concepts such as the use of medications to achieve reduction in tobacco use, chemoprevention to reduce disease, modifications of tobacco products to reduce toxicity, and behavioral approaches to change smoking and tobacco use behavior. Within each of these broad domains, diverse approaches have been suggested. To facilitate clear discussion and analysis, and to avoid confusion among approaches, we catalog 19 approaches to harm reduction, distinguishing and discussing them on 11 dimensions, including their objectives, mechanisms, toxicology, expected population risks, and consumer appeal. Because there have also been so many suggested applications of medicinal nicotine to smoking intervention, we separately catalog and analyze nine applications, some of which constitute new approaches to harm reduction. The suggested framework is intended to clarify the debate, provide for common nomenclature, and facilitate analysis of diverse approaches to tobacco harm reduction.

Harm Reduction↗
PubMed2005

eOPA1: an online database for OPA1 mutations.

Autosomal dominant optic atrophy (ADOA), also known as Kjer disease, is characterized by moderate to severe loss of visual acuity with an insidious onset in early childhood, blue-yellow dyschromatopsia, and central scotoma. An optic atrophy gene, called OPA1, has been identified in most cases of the disease. A total of 83 OPA1 mutations, often family-specific, have been reported so far, and the observations support the hypothesis that haploinsufficiency and the functional loss of a single allele may lead to ADOA. We have developed a new locus-specific database (LSDB), eOPA1 (http://lbbma.univ-angers.fr/eOPA1/) aimed at collecting published and unpublished sequence variations in OPA1. The database has been designed to incorporate new submissions rapidly and will provide a secured online catalog of OPA1 mutations and nonpathogenic sequence variants (NPSVs). The LSDB should prove useful for molecular diagnosis, large-scale mutation statistics, and the determination of original genotype-phenotype correlations in studies on ADOA.

Base Sequence↗
PubMed2005

ISCORS Catalog of References to Parameter Values and Distributions Used in Environmental Pathway Modeling for Cleanup of Sites Contaminated with Radioactivity.

Federal and state regulatory agencies that are concerned with issues of environmental management have adopted approaches toward policy-making that are dose- and risk-informed. To that end they (and others) have developed environmental models and computer codes to mimic the transport of contaminants along air, water, food-chain, and related pathways for estimating potential exposures, doses, and risks to individuals, populations, and ecosystems. Their calculations commonly find application in the planning of remediation, and thereafter in the demonstration of compliance with federal and state cleanup standards. As the models and codes have become more sophisticated, so also have requirements on the accuracy and level of detail of the numerical point values and probability distributions of environmental transfer factors and other parameters that serve as input parameters to them. In response to this growing need, the federal Interagency Steering Committee On Radiation Standards (ISCORS) and the Argonne National Laboratory have developed an on-line, national repository of information on parameter values and distributions of known provenance and demonstrated utility. The ISCORS Catalog of References to Parameter Values and Distributions Used in Environmental Pathway Modeling for Cleanup of Sites Contaminated with Radioactivity is a web-based, indexed compilation of references, compendia, databases, and other sources of peer-reviewed information on parameters. It does not itself contain numerical point values or distributions for any particular parameter, but rather it provides links or directions to sites or other published materials where such information can be obtained. Designed to be user-friendly, easily searchable, and readily up-dateable, the Catalog is being filled, after some initial priming, mainly through on-line submissions of proposed references by the Catalog users themselves. The relevant information on a proposed reference is submitted to ISCORS in a simple, standardized format; it is vetted (with acceptance criteria such as publication in a peer-reviewed technical journal, or appearance in a formally-issued federal agency report) and then added semi-automatically to the Catalog. Built around a relational database, the system offers subject- and text-search capabilities, provides information on parameter definitions and methods of measurement, on transport/exposure pathways, and on standard models and codes. The Catalog is intended for use by (and being populated by) the professionals, managers, and others involved or interested in the application of pathway modeling to estimate doses and risks associated with sites contaminated with radioactive or other hazardous materials.

Databases as Topic↗
PubMed2003

Axiope tools for data management and data sharing.

Many areas of biological research generate large volumes of very diverse data. Managing this data can be a difficult and time-consuming process, particularly in an academic environment where there are very limited resources for IT support staff such as database administrators. The most economical and efficient solutions are those that enable scientists with minimal IT expertise to control and operate their own desktop systems. Axiope provides one such solution, Catalyzer, which acts as flexible cataloging system for creating structured records describing digital resources. The user is able specify both the content and structure of the information included in the catalog. Information and resources can be shared by a variety of means, including automatically generated sets of web pages. Federation and integration of this information, where needed, is handled by Axiope's Mercat server. Where there is a need for standardization or compatibility of the structures usedby different researchers this canbe achieved later by applying user-defined mappings in Mercat. In this way, large-scale data sharing can be achieved without imposing unnecessary constraints or interfering with the way in which individual scientists choose to record and catalog their work. We summarize the key technical issues involved in scientific data management and data sharing, describe the main features and functionality of Axiope Catalyzer and Axiope Mercat, and discuss future directions and requirements for an information infrastructure to support large-scale data sharing and scientific collaboration.

Animals↗
PubMed2005

A comprehensive classification system for lipids.

Lipids are produced, transported, and recognized by the concerted actions of numerous enzymes, binding proteins, and receptors. A comprehensive analysis of lipid molecules, "lipidomics," in the context of genomics and proteomics is crucial to understanding cellular physiology and pathology; consequently, lipid biology has become a major research target of the postgenomic revolution and systems biology. To facilitate international communication about lipids, a comprehensive classification of lipids with a common platform that is compatible with informatics requirements has been developed to deal with the massive amounts of data that will be generated by our lipid community. As an initial step in this development, we divide lipids into eight categories (fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, prenol lipids, saccharolipids, and polyketides) containing distinct classes and subclasses of molecules, devise a common manner of representing the chemical structures of individual lipids and their derivatives, and provide a 12 digit identifier for each unique lipid molecule. The lipid classification scheme is chemically based and driven by the distinct hydrophobic and hydrophilic elements that compose the lipid. This structured vocabulary will facilitate the systematization of lipid biology and enable the cataloging of lipids and their properties in a way that is compatible with other macromolecular databases.

Database Management Systems↗
PubMed1994

Discovering active motifs in sets of related protein sequences and using them for classification.

We describe a method for discovering active motifs in a set of related protein sequences. The method is an automatic two step process: (1) find candidate motifs in a small sample of the sequences; (2) test whether these motifs are approximately present in all the sequences. To reduce the running time, we develop two optimization heuristics based on statistical estimation and pattern matching techniques. Experimental results obtained by running these algorithms on generated data and functionally related proteins demonstrate the good performance of the presented method compared with visual method of O'Farrell and Leopold. By combining the discovered motifs with an existing fingerprint technique, we develop a protein classifier. When we apply the classifier to the 698 groups of related proteins in the PROSITE catalog, it gives information that is complementary to the BLOCKS protein classifier of Henikoff and Henikoff. Thus, using our classifier in conjunction with theirs, one can obtain high confidence classifications (if BLOCKS and our classifier agree) or suggest a new hypothesis (if the two disagree).

Algorithms↗
PubMed2000

Mediation services with health information sources.

OBJECTIVES: To design and implement mediators dedicated to access various kinds of information sources in the framework of the project ARIANE. METHOD: Mediators are dynamically built thanks to three components: pieces of knowledge issued from the UMLS knowledge sources and from a catalog of information sources, processes that translate a query into the syntax of a target source, and communication services provided by operating systems. RESULTS: A scenario details the complete mediation process with an indexed web site. CONCLUSION: This approach mixes knowledge and software engineering. It benefits from services provided by operating systems and allows scalability and reusability of software components.

Computer Communication Networks↗
PubMed2002

Statistics usage in the American Journal of Obstetrics and Gynecology: has anything changed?

OBJECTIVE: Our purpose was to compare statistical listing and usage between articles published in the American Journal of Obstetrics and Gynecology in 1994 with those published in 1999. STUDY DESIGN: All papers included in the obstetrics, fetus-placenta-newborn, and gynecology sections and the transactions of societies sections of the January through June 1999 issues of the American Journal of Obstetrics and Gynecology (volume 180, numbers 1 to 6) were reviewed for statistical usage. Each paper was given a rating for the cataloging of applied statistics and a rating for the appropriateness of statistical usage, when possible. These results were compared with the data collected on a similar review of articles published in 1994. RESULTS: Of the 238 available articles, 195 contained statistics and were reviewed. In comparison to the articles published in 1994, there were significantly more articles that completely cataloged applied statistics (74.3% vs 47.4%) (P <.0001), and there was a significant improvement in appropriateness of statistical usage (56.4% vs 30.3%) (P <.0001). CONCLUSION: Changes in the Instructions to Authors regarding the description of applied statistics and probable changes in the behavior of researchers and Editors have led to an improvement in the quality of statistics in papers published in the American Journal of Obstetrics and Gynecology.

Gynecology↗
PubMedDate not supplied

[French language pharmaceutical publications in 1995. I. Assessment and analysis of French language pharmaceutical periodicals].

Periodicals constitute a vital source of information and an invaluable continuing education medium to pharmacists. The aim of the present study was to compile the list of the 83 pharmacy-related periodicals published in French as at 1995 with a view to establishing their main characteristics. The first part focuses on the definition of the concept of "French language pharmaceutical periodicals" selected for the survey needed a) to be in circulation in 1995 and published at least two times a year, b) published by pharmacists or non-pharmacists but must carry articles intended to help, inform, or retrain pharmacists irrespective of their specialties (community, hospital, biological or industrial pharmacy) as well as their closest collaborators (assistants, technicians, etc.) and c) published in French. The second section presents the methodology of the survey, which consisted essentially in consulting publisher and library catalogs and direct interviews with embassies and Pharmacy Associations in French-speaking countries. Questionnaires were also sent out to editors of periodicals and the information gathered was analysed by computer. The following section reproduces the results of the the survey: These were classified into three categories: scientific, professional, and continuing education periodicals. The last section concentrates on their readership (national, international), frequency, modalities of publication, date of creation, indexing in bibliographic databases.

Language↗
PubMed2003

Self-organization of cognitive performance.

Background noise is the irregular variation across repeated measurements of human performance. Background noise remains after task and treatment effects are minimized. Background noise refers to intrinsic sources of variability, the intrinsic dynamics of mind and body, and the internal workings of a living being. Two experiments demonstrate 1/f scaling (pink noise) in simple reaction times and speeded word naming times, which round out a catalog of laboratory task demonstrations that background noise is pink noise. Ubiquitous pink noise suggests processes of mind and body that change each other's dynamics. Such interaction-dominant dynamics are found in systems that self-organize their behavior. Self-organization provides an unconventional perspective on cognition, but this perspective closely parallels a contemporary interdisciplinary view of living systems.

Adult↗
PubMed2004

Revised nomenclature for the mammalian long-chain acyl-CoA synthetase gene family.

By consensus, the acyl-CoA synthetase (ACS) community, with the advice of the human and mouse genome nomenclature committees, has revised the nomenclature for the mammalian long-chain acyl-CoA synthetases. ACS is the family root name, and the human and mouse genes for the long-chain ACSs are termed ACSL1,3-6 and Acsl1,3-6, respectively. Splice variants of ACSL3, -4, -5, and -6 are cataloged. Suggestions for naming other family members and for the nonmammalian acyl-CoA synthetases are made.

Acyl Coenzyme A↗
PubMed1984

Evaluation of the TALON Cooperative Acquisitions Program for monographs.

The TALON Cooperative Acquisitions Program for monographs (TALON/CAP) was implemented in 1979 by eleven resource libraries in the South Central Regional Medical Library Program. Each participating library acquired books from selected publishers within a profile covering subject and format. The program was evaluated by comparing interlibrary loan requests, surveying participants, and analyzing cataloging records. The results were that ten of the eleven libraries significantly increased their coverage of assigned publishers, and that academic medical libraries are not all buying the same books, even from major medical publishers. The fifty-six publishers in the program accounted for 60% to 83% of the titles with 1977-80 imprints held by participating libraries. The computer-generated collection analysis reports provide a baseline for future collection management studies.

Books↗
PubMed1994

Cytogenetic nomenclature of deer mice, Peromyscus (Rodentia): revision and review of the standardized karyotype. Report of the Committee for the Standardization of Chromosomes of Peromyscus.

A revision of the standardized karyotype of deer mice (Peromyscus) is presented. This revision addresses short-comings of the original standardization, contains a substantial increase in the number of G-band markers and provides a nomenclature for the G-bands of each autosome and the X chromosome. Using the revised standardized karyotype, we specify the particular G-bands or patterns that identify each chromosome and catalog the more problematic chromosome identifications and likely misidentifications. For each chromosome, we present an overview of previously reported variation in euchromatic arrangement and heterochromatic constitution. We then review previous applications of the standardized karyotype and summarize the predominant findings from cytogenetic and cytosystematic studies of Peromyscus and related taxa.

Animals↗
PubMed2002

Documenting the prominence of forensic neuropsychology at national meetings and in relevant professional journals from 1990 to 2000.

Numerous authors have opined that forensic activities have become more prominent within clinical neuropsychology. To investigate the merits of these claims, the entire contents of Archives of Clinical Neuropsychology (ACN), Journal of Clinical and Experimental Neuropsychology (JCEN), and The Clinical Neuropsychologist (TCN) from 1990 through 2000 were reviewed and cataloged. These three journals were selected because they are the highest-ranking clinical subscription journals according to surveys of neuropsychology practitioners. Prior to rating journal content, various categories of interest were delineated and practice ratings were obtained until the two raters reached 92% agreement. Each of the raters read the journal contents and recorded content ratings for half of the journal issues under review. Results of the 8323 ratings demonstrated increases across time in the absolute numbers of articles related to forensic neuropsychology, although variable and different for each journal. Published articles that were partially or substantially forensic in nature in the three journals combined increased from 4% in 1990 to 14% in 2000. An annual peak in absolute number (n=32;16%) of forensic journal articles occurred in 1997. The most common topic of 139 articles published in ACN, JCEN, and TCN from 1990 to 2000 was malingering, which appeared in 86% of the general forensic articles. Forensic presentations at annual NAN meetings ranged from 3.9 to 11.3% (M=8%) of the convention programs, whereas within Division 40's programs at the American Psychological Association meeting, the average percentage ranged from 2.3 to 11.7% (M=6%). Results pertaining to each journal and to specific forensic topics are presented and implications of these and other results are discussed.

Bibliometrics↗
PubMed1998

Towards semantic integration within an existing medical information system.

Talking about the problems of integration in medical information systems, the necessity to provide end users with a consistent and coherent view of patient's data, has been largely reported. In order to attempt this goal, systems need to perform semantic integration. We propose a pragmatic way to describe the semantics of the elements of a database, based on a bottom-up three steps process: 1. a back documentation of the elements of the system from their description contained in the data catalog of the database 2. a first semantic extension to transform a data catalog into a data dictionary 3. a second semantic extension to create a dictionary of the medical concepts from a data dictionary. This dictionary of concepts can be considered as the final result of "semantic integration". It contains a set of entities directly understandable by the end users. These entities are deduced or built from the elements collected and characterized in the data dictionary. This work reports the conceptual analysis and the implementation of such a data dictionary.

Database Management Systems↗
PubMedDate not supplied

Comparison of the NCI open database with seven large chemical structural databases.

Eight large chemical databases have been analyzed and compared to each other. Central to this comparison is the open National Cancer Institute (NCI) database, consisting of approximately 250 000 structures. The other databases analyzed are the Available Chemicals Directory ("ACD," from MDL, release 1.99, 3D-version); the ChemACX ("ACX," from CamSoft, Version 4.5); the Maybridge Catalog and the Asinex database (both as distributed by CamSoft as part of ChemInfo 4.5); the Sigma-Aldrich Catalog (CD-ROM, 1999 Version); the World Drug Index ("WDI," Derwent, version 1999.03); and the organic part of the Cambridge Crystallographic Database ("CSD," from Cambridge Crystallographic Data Center, 1999 Version 5.18). The database properties analyzed are internal duplication rates; compounds unique to each database; cumulative occurrence of compounds in an increasing number of databases; overlap of identical compounds between two databases; similarity overlap; diversity; and others. The crystallographic database CSD and the WDI show somewhat less overlap with the other databases than those with each other. In particular the collections of commercial compounds and compilations of vendor catalogs have a substantial degree of overlap among each other. Still, no database is completely a subset of any other, and each appears to have its own niche and thus "raison d'être". The NCI database has by far the highest number of compounds that are unique to it. Approximately 200 000 of the NCI structures were not found in any of the other analyzed databases.

Cluster Analysis↗