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At least 307 records · Page 17Linked to original sources
PubMed2003

Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes.

Phydbac is a web interactive resource based on phylogenomic profiling, designed to help microbiologists to annotate bacterial proteins. Phylogenomic annotation is based on the assumption that functionally linked protein-coding genes must evolve in a coordinated manner. The detection of subsets of co-evolving genes within a given genome involves the computation of protein sequence conservation profiles across a spectrum of microbial species, followed by the identification of significant pairwise correlations between them. Many ongoing studies are devoted to the problem of computing the most biologically significant phylogenomic profiles and how best identifying clusters of 'functionally interacting' genes. Here we introduce a web tool, Phydbac, allowing the dynamic construction of phylogenomic profiles of protein sequences of interest and their interactive display. In addition, Phydbac can identify Escherichia coli proteins exhibiting the evolution pattern most similar to arbitrary query protein sequences, hence providing functional hints for open reading frames (ORFs) of hypothetical or unknown function. The phylogenomic profiles of all E.coli K-12 protein-coding genes are pre-computed, allowing queries about E.coli genes to be answered instantaneously. The profiles and phylogenomic neighborhoods are computed using an original method shown to perform better than previous ones. An extension of Phydbac, including precomputed profiles for all available bacterial genomes (including major pathogens) will soon be available. Phydbac can be accessed at: http://igs-server.cnrs-mrs.fr/phydbac/.

Bacterial Proteins↗
PubMed2006

Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research.

We have developed a web-based resource (available at www.ciliate.org) for researchers studying the model ciliate organism Tetrahymena thermophila. Employing the underlying database structure and programming of the Saccharomyces Genome Database, the Tetrahymena Genome Database (TGD) integrates the wealth of knowledge generated by the Tetrahymena research community about genome structure, genes and gene products with the newly sequenced macronuclear genome determined by The Institute for Genomic Research (TIGR). TGD provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus in our graphical genome browser, gene product annotations utilizing the Gene Ontology, links to published literature about the gene and more. TGD also displays automatic annotations generated for the gene models predicted by TIGR. A variety of tools are available at TGD for searching the Tetrahymena genome, its literature and information about members of the research community.

Animals↗
PubMed1998

Costs and benefits of connecting community physicians to a hospital WAN.

The Washington Heights-Inwood Community Health Management Information System (WHICHIS) at the Columbia-Presbyterian Medical Center (CPMC) provides 15 community physician practices with seamless networking to the CPMC Wide-Area Network. The costs and benefits of the project were evaluated. Installation costs, including hardware, office management software, cabling, network routers, ISDN connection and personnel time, averaged $22,902 per office. Maintenance and support costs averaged $6,293 per office per year. These costs represent a "best-case" scenario after a several year learning curve. Participating physicians were interviewed to assess the impact of the project. Access to the CPMC Clinical Information System (CIS) was used by 87%. Other resource usage was: non-CPMC Web-based resources, 80%; computer billing, 73%; Medline and drug information databases, 67%; and, electronic mail, 60%. The most valued feature of the system was access to the CPMC CIS. The second most important was the automatic connection provided by routed ISDN. Frequency of access to the CIS averaged 6.67 days/month. Physicians reported that the system had significantly improved their practice of medicine. We are currently exploring less expensive options to provide this functionality.

Attitude of Health Personnel↗
PubMed2005

An Improved Publication Process for the UMVF.

The "Université Médicale Virtuelle Francophone" (UMVF) is a federation of French medical schools. Its main goal is to share the production and use of pedagogic medical resources generated by academic medical teachers. We developed an Open-Source application based upon a workflow system which provides an improved publication process for the UMVF. For teachers, the tool permits easy and efficient upload of new educational resources. For web masters it provides a mechanism to easily locate and validate the resources. For both the teachers and the web masters, the utility provides the control and communication functions that define a workflow system.For all users, students in particular, the application improves the value of the UMVF repository by providing an easy way to find a detailed description of a resource and to check any resource from the UMVF to ascertain its quality and integrity, even if the resource is an old deprecated version. The server tier of the application is used to implement the main workflow functionalities and is deployed on certified UMVF servers using the PHP language, an LDAP directory and an SQL database. The client tier of the application provides both the workflow and the search and check functionalities and is implemented using a Java applet through a W3C compliant web browser. A unique signature for each resource, was needed to provide security functionality and is implemented using the MD5 Digest algorithm. The testing performed by Rennes and Lille verified the functionality and conformity with our specifications.

Education, Medical↗
PubMed2006

An automated approach to studying health resource and infobutton use.

Many studies have found that clinicians require access to medical knowledge sources while viewing data in their patients' health records. To address this need, we have been developing links to various on-line health information resources from our Web-based clinical information system (WebCIS). Clinicians can access these resources through a "Health Resources" Web page or use context-sensitive "infobuttons" that automatically link to specific resources. To assist in understanding how clinicians interact with these two mechanisms, we have been exploring the use of an automated approach to answer questions about usage for guiding the further development of links to resources. In this paper, we discuss the use of a knowledge discovery technique (CIS Usage Mining) to obtain usage statistics from log files that record interactions with health resources and infobuttons in WebCIS, describe a Web-based interface developed to present the results, and summarize how the results could be applied. The availability of effective links to on-line medical knowledge sources from the patient health record can assist in resolving information needs, potentially improving patient care and decision-making.

Access to Information↗
PubMed2002

Recent improvements to the SMART domain-based sequence annotation resource.

SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with particular emphasis on mobile eukaryotic domains. Extensive annotation for each domain family is available, providing information relating to function, subcellular localization, phyletic distribution and tertiary structure. The January 2002 release has added more than 200 hand-curated domain models. This brings the total to over 600 domain families that are widely represented among nuclear, signalling and extracellular proteins. Annotation now includes links to the Online Mendelian Inheritance in Man (OMIM) database in cases where a human disease is associated with one or more mutations in a particular domain. We have implemented new analysis methods and updated others. New advanced queries provide direct access to the SMART relational database using SQL. This database now contains information on intrinsic sequence features such as transmembrane regions, coiled-coils, signal peptides and internal repeats. SMART output can now be easily included in users' documents. A SMART mirror has been created at http://smart.ox.ac.uk.

Animals↗
PubMed2006

sgTarget: a target selection resource for structural genomics.

sgTarget (http://www.ysbl.york.ac.uk/sgTarget) is a web-based resource to aid the selection and prioritization of candidate proteins for structure determination. The system annotates user submitted gene or protein sequences, identifying sequence families with no homologues of known structure, and characterizing each protein according to a range of physicochemical properties that may affect its expression, solubility and likelihood to crystallize. Summaries of these analyses are available for individual sequences, as well as whole datasets. This type of analysis enables structural biologists to iteratively select targets from their genomic sequences of interest and according to their research needs. All sequence datasets submitted to sgTarget are available for users to select and rank using their choice of criteria. sgTarget was developed to support individual laboratories collaborating in structural and functional genomics projects and should be valuable to structural biologists wishing to employ the wealth of available genome sequences in their structural quests.

Animals↗
PubMed2006

Web-based climate information resources for malaria control in Africa.

Malaria remains a major public health threat to more than 600 million Africans and its control is recognized as critical to achieving the Millennium Development Goals. The greatest burden of malaria in Africa occurs in the endemic regions where the disease pathogen is continuously present in the community. These regions are characterized by an environment that is conducive to interactions between the Anopheles mosquito, malaria parasites and human hosts, as well as housing of generally poor quality, which offers little protection from mosquito-human contact. Epidemic malaria tends to occur along the geographical margins of endemic regions, when the equilibrium between the human, parasite and mosquito vector populations is occasionally disturbed and a sharp but temporary increase in disease incidence results. When malaria control measures are inadequate, as is the case in much of sub-Saharan Africa, the disease distribution is closely linked with seasonal patterns of the climate and local environment. In the absence of good epidemiological data on malaria distribution in Africa, climate information has long been used to develop malaria risk maps that illustrate the boundaries of 'climatic suitability for endemic transmission.' The best known of these are produced by the Pan-African-based MARA Collaboration. This paper describes the development of additional malaria suitability maps which have been produced in an online, interactive format to enable temporal information (i.e., seasonality of climate conditions) to be queried and displayed along with spatial information. These maps and the seasonal information that they contain should be useful to the malaria control and health service communities for their planning and operational activities.

Africa↗
PubMed2005

Pathway and ontology analysis: emerging approaches connecting transcriptome data and clinical endpoints.

The increasing use of gene expression profiling offers great promise in clinical research into disease biology and its treatment. Along with the ability to measure changing expression levels in thousands of genes at once, comes the challenge of analyzing and interpreting the vast sets of data generated. Analysis tools are evolving rapidly to meet such challenges. The next step is to interpret observed changes in terms of the biological properties or relationships underlying them. One powerful approach is to make associations between the genes that are under investigation and well-known biochemical or signaling pathways, and further to assess the significance of such associations. Similarly, genes can be mapped to standardized biological categories via an ontology resource. We discuss these approaches and several web-based resources and tools designed to facilitate such analyses. This information can be used to facilitate understanding and to help design more focused experiments for validating the relevance and importance of these biological pathways and processes in human disease and therapeutics.

Animals↗
PubMed2005

Clinical Decision Support Systems (CDSS) in GRID Environments.

This paper presents an architecture defined for searching and executing Clinical Decision Support Systems (CDSS) in a LCG2/GT2 Grid environment, using web-based protocols. A CDSS is a system that provides a classification of the patient illness according to the knowledge extracted from clinical practice and using the patient's information in a structured format. The CDSS classification engines can be installed in any site and can be used by different medical users from a Virtual Organization (VO). All users in a VO can consult and execute different classification engines that have been installed in the Grid independently of the platform, architecture or site where the engines are installed or the users are located. The present paper present a solution to requirements such as short-job execution, reducing the response delay on LCG2 environments and providing grid-enabled authenticated access through web portals. Resource discovering and job submission is performed through web services, which are also described in the article.

Classification↗
PubMed2000

Allochthonous inputs: integrating population changes and food-web dynamics.

Most ecosystems are recipients of allochthonous materials that enhance in situ productivity. Recent theoretical and empirical studies suggest that low to moderate inputs can stabilize food webs. However, depending on the trophic levels that use the resource, food webs can become unstable as inputs increase. Where large amounts of agricultural resources are transferred to natural habitats, trophic dynamics change: trophic cascades can occur and rare or uncommon species can become invasive. Rates of change in species abundances can also be amplified by the effects of changes in legislation and management practices on subsidized consumers.

Journal Article↗
PubMed1996

World Wide Web-based access to heterogenous information resources for cytokine research and education.

Cytokines are currently the focus of intense research efforts, and information related to cytokine biology is expanding at an extremely rapid rate. The primary literature has become insufficient as a source for timely information, and efficient searches of the older literature are complicated by the nature of cytokine nomenclature. A few computer-accessible cytokine-related data sources have recently been developed, but these are typically limited in scope and not integrated with other information resources. We have developed Cytokine Explorer, a World Wide Web (WWW)-based resource to provide access to and guidance in use of information for research and education in cytokine biology. The resource consists of: (1) a searchable thesaurus of cytokine nomenclature; (2) a cytokine reagent database containing information from academic institutions and commercial sources; (3) a set of links to cytokine-related WWW sites; and (4) a database of functional information retrieval maps for guided retrieval of cytokine information from combinations of heterogeneous sources.

Computer Communication Networks↗
PubMed2002

International use of an academic nephrology World Wide Web site: from medical information resource to business tool.

BACKGROUND: Studies of the use of the World Wide Web to obtain medical knowledge have largely focused on patients. In particular, neither the international use of academic nephrology World Wide Web sites (websites) as primary information sources nor the use of search engines (and search strategies) to obtain medical information have been described. METHODS: Visits ("hits") to the Walter Reed Army Medical Center (WRAMC) Nephrology Service website from April 30, 2000, to March 14, 2001, were analyzed for the location of originating source using Webtrends, and search engines (Google, Lycos, etc.) were analyzed manually for search strategies used. RESULTS: From April 30, 2000 to March 14, 2001, the WRAMC Nephrology Service website received 1,007,103 hits and 12,175 visits. These visits were from 33 different countries, and the most frequent regions were Western Europe, Asia, Australia, the Middle East, Pacific Islands, and South America. The most frequent organization using the site was the military Internet system, followed by America Online and automated search programs of online search engines, most commonly Google. The online lecture series was the most frequently visited section of the website. Search strategies used in search engines were extremely technical. CONCLUSIONS: The use of "robots" by standard Internet search engines to locate websites, which may be blocked by mandatory registration, has allowed users worldwide to access the WRAMC Nephrology Service website to answer very technical questions. This suggests that it is being used as an alternative to other primary sources of medical information and that the use of mandatory registration may hinder users from finding valuable sites. With current Internet technology, even a single service can become a worldwide information resource without sacrificing its primary customers.

District of Columbia↗