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Mining environmental toxicology information: web resources.

Environmental toxicology is the study of the ecological effects of anthropogenic substances released into the environment. It is a relatively diverse field addressing impacts to aquatic and terrestrial organisms and communities. The determination of potential risk associated with toxic agents is of interest to government regulators, industry, researchers, private organizations and citizen groups. In assessing the ecological risk associated with a chemical stressor, it is important to establish linkages between likely exposure concentrations and adverse effects to ecological receptors. To do so requires access to reliable information resources. The proper application of such data requires familiarity with the scientific literature and keeping abreast of new and emerging issues as well as state-of-the-art research findings and methods. In addition, an understanding of government regulations as they relate to environmental issues is also of primary interest. The advent of the Web has made these tools accessible at computer desktops. This review focuses on currently available free Web resources related to environmental toxicology, specifically those which address available empirical data sources, predictive tools and publications of interest such as standard test methods, guidance documents and governmental regulations.

Animals↗

IMGT databases, web resources and tools for immunoglobulin and T cell receptor sequence analysis, http://imgt.cines.fr.

IMGT, the international ImMunoGeneTics database((R)) (http://imgt.cines.fr), is a high-quality integrated information system specializing in immunoglobulins (IG), T cell receptors (TR) and major histocompatibility complex (MHC) of human and other vertebrates, created in 1989, by LIGM, at the Université Montpellier II, CNRS, Montpellier, France. IMGT provides a common access to standardized data which include nucleotide and protein sequences, oligonucleotide primers, gene maps, genetic polymorphisms, specificities, 2D and 3D structures. IMGT includes several databases (IMGT/LIGM-DB, IMGT/3Dstructure-DB, IMGT/HLA-DB), Web resources ('IMGT Marie-Paule page') and interactive tools (IMGT/V-QUEST, IMGT/JunctionAnalysis). IMGT expertly annotated data and tools described in this paper are particularly useful for the analysis of the IG and TR rearrangements in leukemia, lymphoma and myeloma, and in translocations involving the antigen receptor loci. IMGT is freely available at http://imgt.cines.fr.

Amino Acid Sequence↗

IMGT-ONTOLOGY and IMGT databases, tools and Web resources for immunogenetics and immunoinformatics.

The international ImMunoGeneTics information system (IMGT; http://imgt.cines.fr), is a high quality integrated information system specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), and related proteins of the immune system (RPI) of human and other vertebrates, created in 1989, by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM; Université Montpellier II and CNRS) at Montpellier, France. IMGT provides a common access to standardized data which include nucleotide and protein sequences, oligonucleotide primers, gene maps, genetic polymorphisms, specificities, 2D and 3D structures. IMGT consists of several sequence databases (IMGT/LIGM-DB, IMGT/MHC-DB, IMGT/PRIMER-DB), one genome database (IMGT/GENE-DB) and one 3D structure database (IMGT/3Dstructure-DB), interactive tools for sequence analysis (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/PhyloGene, IMGT/Allele-Align), for genome analysis (IMGT/GeneSearch, IMGT/GeneView, IMGT/LocusView) and for 3D structure analysis (IMGT/StructuralQuery), and Web resources ("IMGT Marie-Paule page") comprising 8000 HTML pages. IMGT other accesses include SRS, FTP, search by BLAST, etc. By its high quality and its easy data distribution, IMGT has important implications in medical research (repertoire in autoimmune diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research, genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (single chain Fragment variable (scFv), phage displays, combinatorial libraries) and therapeutical approaches (grafts, immunotherapy). IMGT is freely available at http://imgt.cines.fr.

Animals↗

ORENZA: a web resource for studying ORphan ENZyme activities.

BACKGROUND: Despite the current availability of several hundreds of thousands of amino acid sequences, more than 36% of the enzyme activities (EC numbers) defined by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) are not associated with any amino acid sequence in major public databases. This wide gap separating knowledge of biochemical function and sequence information is found for nearly all classes of enzymes. Thus, there is an urgent need to explore these sequence-less EC numbers, in order to progressively close this gap. DESCRIPTION: We designed ORENZA, a PostgreSQL database of ORphan ENZyme Activities, to collate information about the EC numbers defined by the NC-IUBMB with specific emphasis on orphan enzyme activities. Complete lists of all EC numbers and of orphan EC numbers are available and will be periodically updated. ORENZA allows one to browse the complete list of EC numbers or the subset associated with orphan enzymes or to query a specific EC number, an enzyme name or a species name for those interested in particular organisms. It is possible to search ORENZA for the different biochemical properties of the defined enzymes, the metabolic pathways in which they participate, the taxonomic data of the organisms whose genomes encode them, and many other features. The association of an enzyme activity with an amino acid sequence is clearly underlined, making it easy to identify at once the orphan enzyme activities. Interactive publishing of suggestions by the community would provide expert evidence for re-annotation of orphan EC numbers in public databases. CONCLUSION: ORENZA is a Web resource designed to progressively bridge the unwanted gap between function (enzyme activities) and sequence (dataset present in public databases). ORENZA should increase interactions between communities of biochemists and of genomicists. This is expected to reduce the number of orphan enzyme activities by allocating gene sequences to the relevant enzymes.

Amino Acid Sequence↗

World Wide Web resources for perinatal nursing.

The article provides practical guidelines on how to access and search for information resources on topics related to perinatal nursing on the World Wide Web. Categorized listings of key information sites include major relevant databases and bibliographies, electronic journals, sites relevant to perinatal nursing, and community health resources. The Web provides an excellent information resource for health care professionals and the public to gain practical clinical knowledge and to access research resources. Internet technology has altered the way data are perceived and presented because of the speed with which complex data manipulations are now possible and on account of the vast quantities of data involved.

Databases, Bibliographic↗

World Wide Web resources for the biologist.

The World Wide Web is currently the major networking resource for biologists. It has passed Gopher and simple electronic mail (email) servers in popularity. In the 1990s, the advent of client-server software will be the main driving force in bioinformatics. During the past few years, biologists have used the Internet increasingly to distribute data, and the methods of doing this have become more and more sophisticated as the speed with which network links can be made has increased.

Biology↗

Health and medical news on the Web: comparing the results of news-providing Web resources.

News changes constantly. That change and the abundance of Web-based news resources available complicate finding the news. This paper reviews sixteen different online news sources for their coverage of recent health and medical issues; both general-interest and medical news sites are included. Three health-related news stories were searched in all resources within set time-frames to provide a comparison of coverage. Features and types of resources are described. The use of RSS feeds and weblogs to find news is also discussed with suggestions for using news aggregators to control the flow of information.

Internet↗

Web resources for drug toxicity.

Information on drug toxicity is used primarily by three segments of the health care industry: the consumer or patient, healthcare practitioners, and research and development (R&D) scientists in the pharmaceutical industry. The major focus of both consumers and health care practitioners is the provision of suitable information for the safe use of drugs for both individuals and specific patient populations. Therefore, accurate information on potential side effects and drug-drug and food-drug interactions is critical. For pharmaceutical scientists, the use of toxicity information is more complex and has become an essential part of the R&D process. The high rate of failures in drug development has precipitated the utilization of all available resources to gather relevant information that may improve the process of drug development. The web is a growing source of information and services for the pharmaceutical industry. Web-based resources for non-clinical drug development include tools for virtual discovery such as silico ADME/Toxicity programs, access to information regarding in vitro and in vivo testing, new data management options, and the latest regulatory guidelines and industry news. These resources are reviewed from the perspective of a toxicologist.

Animals↗

Forensic toxicology: web resources.

Forensic toxicology is the study and practice of the application of toxicology to the purposes of the law. The internet provides abundant web-sites and resources for the practicing forensic toxicologist and those interested in the field of forensic toxicology. This review includes a description of web-sites, databases of toxicological and analytical data, and web-based journals, forums and mailing lists.

Databases as Topic↗

ESEfinder: A web resource to identify exonic splicing enhancers.

Point mutations frequently cause genetic diseases by disrupting the correct pattern of pre-mRNA splicing. The effect of a point mutation within a coding sequence is traditionally attributed to the deduced change in the corresponding amino acid. However, some point mutations can have much more severe effects on the structure of the encoded protein, for example when they inactivate an exonic splicing enhancer (ESE), thereby resulting in exon skipping. ESEs also appear to be especially important in exons that normally undergo alternative splicing. Different classes of ESE consensus motifs have been described, but they are not always easily identified. ESEfinder (http://exon.cshl.edu/ESE/) is a web-based resource that facilitates rapid analysis of exon sequences to identify putative ESEs responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements.

Base Sequence↗

Web resources for patients with prostate cancer: a starting point.

The information available on the World Wide Web is vast. Patients are becoming increasingly interested in resources available to them on the Internet for health and medical information. As the percentage of Americans with Internet access grows, health care providers are being asked by their patients to facilitate the search for quality information. This article provides the groundwork for urologists counseling their patients about Web-based information on prostate cancer. Internet sites that provide clear, in-depth information about symptoms and characteristics of prostate cancer, common tests performed, prevention, and treatment options are reviewed. Ten high-quality, patient-friendly Web sites that may be used as a resource for patients and physicians are presented.

Decision Making↗

Web resources for HIV type 1 genotypic-resistance test interpretation.

Interpreting the results of plasma human immunodeficiency virus type 1 (HIV-1) genotypic drug-resistance tests is one of the most difficult tasks facing clinicians caring for HIV-1-infected patients. There are many drug-resistance mutations, and they arise in complex patterns that cause varying levels of drug resistance. In addition, HIV-1 exists in vivo as a virus population containing many genomic variants. Genotypic-resistance testing detects the drug-resistance mutations present in the most common plasma virus variants but may not detect drug-resistance mutations present in minor virus variants. Therefore, interpretation systems are necessary to determine the phenotypic and clinical significance of drug-resistance mutations found in a patient's plasma virus population. We describe the scientific principles of HIV-1 genotypic-resistance test interpretation and the most commonly used Web-based resources for clinicians ordering genotypic drug-resistance tests.

Anti-HIV Agents↗

Interactive cell modeling web-resource, iCell, as a simulation-based teaching and learning tool to supplement electrophysiology education.

An interactive cell modeling web site, iCell (http://ssd1.bme.memphis.edu/icell/), that integrates research and education, was developed to present and to disseminate JAVA-coded models of cellular activities, and to supplement physiology education. iCell can be used to supplement the text-book material as a simulation-based teaching and learning tool. Specifically, iCell allows the students to supplement their learning experiences of the text-book cellular physiology material by running simulations in an interactive environment. The site consists of JAVA-coded models of various cardiac cells and neurons, and provides simulation data of their bioelectric transport activities at cellular level. Each JAVA-coded model allows the user to go through menu options to change model parameters, run and view simulation results. The site also has a glossary section for the scientific terms. iCell has been used as a teaching and learning tool for seven graduate courses at the Joint Biomedical Engineering Program of University of Memphis and University of Tennessee. This modeling tool was also used as a collaboration site among our physiology colleagues interested in simulations of cell membrane activities. Scientists from the fields of biosciences, engineering, life sciences and medical sciences in 17 countries have tested and utilized iCell as a simulation-based teaching, learning and collaboration environment. iCell provides us with an interactive, platform-independent, and user-friendly teaching and learning resource, and also a collaboration environment for electrophysiology to be shared over the Internet. The usage of simulations for teaching and learning will continue advancing simulation-based engineering and sciences for research and development.

Animals↗

TOXNET: an evolving web resource for toxicology and environmental health information.

TOXNET, developed by the National Library of Medicine (NLM), is a web-based system of databases providing information on toxicology, hazardous chemicals, and the environment. Databases fall under the general headings of Toxicology Data, Toxicology Literature, Toxic Releases, and Chemical Identification/Nomenclature. Among TOXNET's pre-eminent databases are the Hazardous Substances Data Bank (HSDB) and the TOXLINE file of bibliographic references.

Environmental Health↗

Internet Web resources for anti-tobacco advocacy.

The Internet has recently witnessed growth since it became accessible to the common user in 1990. It is becoming a valuable communications and information resource for the anti-tobacco movement. This article summarizes many valuable resources for the anti-tobacco activist to be found on the World Wide Web today.

Computer Communication Networks↗

EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes.

EPConDB (http://www.cbil.upenn.edu/EPConDB) is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in cells of the pancreas. EPConDB displays expression profiles for individual genes and information about transcripts, promoter elements and transcription factor binding sites. Gene expression results are obtained from studies examining tissue expression, pancreatic development and growth, differentiation of insulin-producing cells, islet or beta-cell injury, and genetic models of impaired beta-cell function. The expression datasets are derived using different microarray platforms, including the BCBC PancChips and Affymetrix gene expression arrays. Other datasets include semi-quantitative RT-PCR and MPSS expression studies. For selected microarray studies, lists of differentially expressed genes, derived from PaGE analysis, are displayed on the site. EPConDB provides database queries and tools to examine the relationship between a gene, its transcriptional regulation, protein function and expression in pancreatic tissues.

Animals↗

Web resources for the carbohydrate chemist.

Bioinformatics has played a pivotal role in advancing genetics and protein sciences. The large amount of information generated by genomics, and now proteomics, has been a driving force. By comparison, glycobiology still generates small amounts of data. The need to organize our knowledge about carbohydrates is however growing constantly and has given rise to an increasing number of public databases and freely available tools. This review gives an overview of the carbohydrate-oriented resources currently available on the Internet. Many of the resources are seldom referred to in the literature and difficult to find, in part because of the constant flux of the net itself, but also because many efforts have been lead by a single individual. As the World Wide Web has matured the number of 'permanent' resources, maintained by organizations rather than individuals, has increased. In this paper, we present some of the more useful and accessible public tools and databases. There are also a few commercial initiatives but these have not been reviewed.

Biochemical Phenomena↗

RE-AIM: evidence-based standards and a Web resource to improve translation of research into practice.

BACKGROUND: Health services data indicate that under present conditions evidence-based medical and preventive practices are not consistently implemented in clinical practice and affect the quality of care provided to patients. Operating with similar conditions and resources, it is unlikely that evidence-based behavioral medicine (EBBM) practices will be more successfully implemented. PURPOSE: In this article we propose ways to help improve the implementation of EBBM practice. METHODS: This article describes the RE-AIM (Reach, Efficacy/Effectiveness, Adoption, Implementation, and Maintenance) framework that is available on a free-use Web site (http://www.re-aim.org), which offers practical research translation tools, resources, and support for program planners, community leaders, and researchers. The material located at www.re-aim.org can be used to help anticipate and overcome likely barriers to dissemination and to estimate eventual public health impact. RESULTS: Data on Web site utilization and lessons learned thus far in its implementation are presented. CONCLUSIONS: Scientists and public health leaders should devote greater attention to reporting practice-oriented issues such as generalizability, breadth of application, and pragmatic and setting or contextual issues in addition to the current focus on internal validity issues. We hope that this and similar efforts will assist EBBM interventions to have broader applications, be consistently implemented, and be sustained.

Behavioral Medicine↗