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At least 379 records · Page 21Linked to original sources

PubMedDate not supplied

Where are they now? A case study of health-related Web site attrition.

BACKGROUND: When considering health-related Web sites, issues of quality generally focus on Web content. Little concern has been given to attrition of Web sites or the "fleeting" nature of health information on the World Wide Web. Since Web sites may be available for an uncertain period of time, a Web page may not be a sound reference. OBJECTIVE: To address the issue of attrition, a defined set of health-related Web sites was examined at two separate time intervals. METHODS: To determine the degree of attrition, Web sites obtained and recorded from a previous study were revisited approximately three years later. From December 1998 to May 1999, 184 Web sites were collected from which health claims were identified. During May and June 2002, the previously recorded URL for each Web site was entered into the address field of the browser Netscape Navigator. It was documented whether the original Web site could not be found, moved to a different URL location, or the URL and site location was found unchanged from the original search. For a Web site whose URL remained unchanged, it was also noted whether the site had maintained currency, (i.e. updated) since the original posting. To ensure that inaccessibility may not be due to temporary server problems, another attempt was made to access the sites at different periods of time. RESULTS: When each URL address from the original set of 184 Web sites was re-entered into the address field of the browser, 108 (59%) of the sites could not be found, 31 (17%) had moved to a new URL address, and 45 (24%) of the sites could be found from the original URLs obtained in the previous study. Of the Web sites that moved to a new URL address, 7 sites provided a link from the original URL to redirect the viewer to the new location. Of the Web sites still in existence, 17 (38%) provided update information from the original posting. CONCLUSIONS. It can be difficult to locate information that was previously found on the Web, and if a reference to an item is provided, there is no guarantee that viewers will be able to find the site at a later time. Enhancements in Web technologies such as the Internet Archive may improve this situation. Future research that is directed toward making sure Web site viewers know the site will be accessible at a later time will enhance the Web as a valuable medical information resource.

Humans↗

PubMed2005

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays.

BACKGROUND: The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH). One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. RESULTS: We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment) supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. CONCLUSION: ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at http://medgen.ugent.be/arrayCGHbase/.

Base Sequence↗

PubMed2000

The integrity of Web-delivered experiments: can you trust the data?

Data from Web-delivered experiments conducted in browsers by remote users of PsychExperiments, a public on-line psychology laboratory, reveal experiment effects that mirror lab-based findings, even for experiments that require nearly millisecond accuracy of displays and responses. Textbook results are obtained not just for within-subjects effects, but for between-subjects effects as well. These results suggest that existing technology is adequate to permit Web delivery of many cognitive and social psychological experiments and that the added noise created by having participants in different settings using different computers is easily compensated for by the sample sizes achievable with Web delivery.

Bias↗

PubMed2001

[Efficient multicentric data acquisition via internet - a method evaluation].

Data input in web-htm-forms with a browser is much more efficient in comparison with write in paper mask documents. The specification-compliant forms for data entry as htm-forms are downloaded from the homepage of the project manager by the participants of the study. The transformation of content of different formatted htm-forms is made by the program "security-based form converter (SFC)", which is located on a web server respectively a proxy server. From there the transformed data are returned the project manager via e-mail. Those incoming data are imported into databases by means of ODBC-data source. The data are pivoted from sequential format to table format. The data entry principle presented here is a client-server-structured, web based intranet program. For this purpose only standard software and relational databases with ODBC-interfaces are used; no further registered commercial programs are needed. General data protection is ensured by encrypted data transmission.

Computer Security↗

PubMed1998

Disseminating multimedia protocols over Internet for emergency and catastrophe management.

Over the last years we have developed various computing methods to assist specialized personnel on various aspects of catastrophe and emergency management. New models can address tasks such as patient triage; stabilization, resource coordination and hospital alertness and techniques based on information technologies. In this paper we present various tools (written on Java and C+2) that we created to store, represent, and disseminate practice guidelines and protocols over the World Wide Web. Guidelines and protocols are stored using a standard database program (e.g., Microsoft Access), and represented in a flowchart format linked to multimedia information such as text, pictures, sound, video or external sources of data. Using our JAVA tool, protocols can be disseminated over the Web and viewed with any browser with JAVA compliance. We have implemented 15 emergency protocols that we developed in collaboration with specialized military personnel from the Ministry of Defense, Spain. Users can access remotely those electronic protocols comparing their procedures and methods. Our goal is to enhance agreement and consensus among remote medical centers regarding emergency and catastrophe management, establishing discussions over the network. Our tools have also a potential for training medical and paramedical personnel for emergency situations.

Clinical Protocols↗

PubMed2001

Knowledge-based interpretation of toxoplasmosis serology test results including fuzzy temporal concepts--the ToxoNet system.

Transplacental transmission of Toxoplasma gondii from an infected, pregnant woman to the unborn that occurs with a probability of about 60 percent [1] results in fetal damage to a degree depending on the gestational age. The computer system ToxoNet processes the results of serological antibody tests having been performed during pregnancy by means of a knowledge base containing medical knowledge on the interpretation of Toxoplasmosis serology tests. By applying this knowledge ToxoNet generates interpretive reports consisting of a diagnostic interpretation and recommendations for therapy and further testing. For that purpose it matches the results of all serological investigations of maternal blood with the content of the knowledge base returning complete textual interpretations for all given findings. The interpretation algorithm derives the stage of maternal infection from these that is used to infer the degree of fetal threat. To consider varying immune responses of particular patients, certain time intervals have to be kept between two subsequent tests in order to guarantee a correct interpretation of the test results. These time intervals are modelled as fuzzy sets, since they allow the formal description of the temporal uncertainties. ToxoNet comprises the knowledge base, an interpretation system, and a program for the creation and modification of the knowledge base. It is available from the World Wide Web by starting a standard browser like the Internet Explorer or the Netscape Navigator. Thus ToxoNet supports the physician in Toxoplasmosis diagnostics and in addition allows to adopt the way of making decisions to the characteristics of the particular laboratory by modifying the underlying knowledge base.

Algorithms↗

PubMed2002

Design and development of an Internet registry for congenital heart defects.

BACKGROUND: Congenital Heart Defects (CHD) are conditions that encompass more than 50 diagnoses and are due to developmental abnormalities early in fetal life. The King Faisal Specialist Hospital and Research Centre in the Kingdom of Saudi Arabia treats approximately 100 new cases per month. We recently developed a new CHD Registry that captures, stores and processes our data via the Internet. METHODS: The Registry was developed using Hypertext Markup Language (HTML), Microsoft Active Server Pages and Microsoft Structured Query Language (SQL). RESULTS: Details of CHD cases are captured in a World Wide Web (WWW) Registry, permitting any browser-enabled PC or Mac to participate fully in all registry functions, including data-entry, viewing, editing, searching, reporting, validating, charting, and exporting data subsets to statistics packages. It includes "administrative" features and an active security system. The paper forms have been designed to reflect the "look and feel" of the Web pages. Automatic validation procedures are also included. CONCLUSIONS: Our Registry has been in operation for 3 years. It serves 10 PCs and contains more than 3,000 registered cases of CHD. It is the first CHD Registry to be fully functional on the Internet. It is also the first dedicated CHD registry, and the first to routinely report on the full spectrum of CHD diagnoses. The WWW offers several logistical advantages to disease registries, especially those that represent large regions. It also offers the possibility of sharing resources between registries, facilitating the aggregation and analysis of disease data on a world-wide scale. This is useful for rare diseases such as CHD (see http://rc.kfshrc.edu.sa/chdr/demo/).

Adolescent↗

PubMed2026

GRNContext: an interactive web platform for contextualized gene regulatory networks visualization across human cancers.

SUMMARY: While current Gene Regulatory Network (GRN) databases provide comprehensive reference maps of potential interactions between transcription factors and target genes, they do not specify which regulatory interactions are active within specific biological contexts. This limitation is particularly critical in cancer, where transcriptional programs are inherently tissue-specific. To address this gap, we developed GRNContext, an interactive web platform designed for the visualization, exploration, and comparative analysis of gene regulatory networks contextualized across 33 cancer types from The Cancer Genome Atlas (TCGA). Our approach uses the TFLink human reference GRN as a starting point and integrates TCGA transcriptomic profiles to infer cancer-specific regulatory activity. Regulatory relevance was assessed using complementary machine learning and statistical methods, which were unified into a consensus score to prioritize and filter the most relevant candidate regulators for each target gene. By providing both curated context-specific GRNs and a user-friendly platform, GRNContext constitutes a comprehensive and accessible resource that supports mechanistic investigations, hypothesis generation, and translational research focused on transcriptional regulation in cancer. AVAILABILITY AND IMPLEMENTATION: GRNContext is supported by all major browsers and freely available on the web at https://apps.cienciavida.org/grncontext. It is implemented as a client-server web application featuring a FastAPI backend and a React frontend utilizing Cytoscape.js for interactive network visualization, all containerized via Docker for cross-platform compatibility.

Humans↗

PubMed2005

GeneCruiser: a web service for the annotation of microarray data.

SUMMARY: GeneCruiser is a web service allowing users to annotate their genomic data by mapping microarray feature identifiers to gene identifiers from databases, such as UniGene, while providing links to web resources, such as the UCSC Genome Browser. It relies on a regularly updated database that retrieves and indexes the mappings between microarray probes and genomic databases. Genes are identified using the Life Sciences Identifier standard. AVAILABILITY: GeneCruiser is freely available in the following forms: Web service and Web application, http://www.genecruiser.org; GenePattern, GeneCruiser access has been integrated into our microarray analysis platform, GenePattern. http://www.genepattern.org.

Animals↗

PubMed2000

Structure and presentation of a World Wide Web database of CSF virus isolates held at the EU reference laboratory.

A computerized database was generated with the epidemiological data of more than 600 CSF virus strains and isolates kept in the EU Reference Laboratory for Classical Swine Fever in Hanover. In addition, as sequence data from defined regions of the genome are increasingly being used for genetic typing of new isolates and are thus being published, it was decided to integrate them into the database. In order to make the epidemiological and the sequence data available to other laboratories through the World Wide Web, a searchable web interface was programmed, which can be accessed using an Internet browser like Netscape or Internet Explorer. The possibility to exchange data via the web has the potential to increase our knowledge concerning genetic and epidemiological links between outbreaks worldwide.

Animals↗

PubMed2004

rVISTA 2.0: evolutionary analysis of transcription factor binding sites.

Identifying and characterizing the transcription factor binding site (TFBS) patterns of cis-regulatory elements represents a challenge, but holds promise to reveal the regulatory language the genome uses to dictate transcriptional dynamics. Several studies have demonstrated that regulatory modules are under positive selection and, therefore, are often conserved between related species. Using this evolutionary principle, we have created a comparative tool, rVISTA, for analyzing the regulatory potential of noncoding sequences. Our ability to experimentally identify functional noncoding sequences is extremely limited, therefore, rVISTA attempts to fill this great gap in genomic analysis by offering a powerful approach for eliminating TFBSs least likely to be biologically relevant. The rVISTA tool combines TFBS predictions, sequence comparisons and cluster analysis to identify noncoding DNA regions that are evolutionarily conserved and present in a specific configuration within genomic sequences. Here, we present the newly developed version 2.0 of the rVISTA tool, which can process alignments generated by both the zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from the ECR Browser and GALA database. The rVISTA web server is closely interconnected with the TRANSFAC database, allowing users to either search for matrices present in the TRANSFAC library collection or search for user-defined consensus sequences. The rVISTA tool is publicly available at http://rvista.dcode.org/.

Algorithms↗

PubMed1998

The Merck Gene Index browser: an extensible data integration system for gene finding, gene characterization and EST data mining.

MOTIVATION: To make effective use of the vast amounts of expressed sequence tag (EST) sequence data generated by the Merck-sponsored EST project and other similar efforts, sequences must be organized into gene classes, and scientists must be able to 'mine' the gene class data in the context of related genomic data. RESULTS: This paper presents the Merck Gene Index browser, an easily extensible, World Wide Web-based system for mining the Merck Gene Index (MGI) and related genomic data. The MGI is a non-redundant set of clones and sequences, each representing a distinct gene, constructed from all high-quality 3' EST sequences generated by the Merck-sponsored EST project. The MGI browser integrates data from a variety of sources and storage formats, both local and remote, using an eclectic integration strategy, including a federation of relational databases, a local data warehouse and simple hypertext links. Data currently integrated include: LENS cDNA clone and EST data, dbEST protein and non-EST nucleic acid similarity data, WashU sequence chromatograms. Entrez sequence and Medline entries, and UniGene gene clusters. Flatfile sequence data are accessed using the Bioapps server, an internally developed client-server system that supports generic sequence analysis applications. Browser data are retrieved and formatted by means of the Bioinformatics Data Integration Toolkit (B-DIT), a new suite of Perl routines.

Abstracting and Indexing↗

PubMed2004

Use of web-enabled databases for complex animal health investigations.

Web-enabled databases developed in the late 1990s to help organise large web sites and allow data capture via browser-based forms. By enabling users outside a closed network access to a central database, they permit greater flexibility than traditional 'client-server' systems. Accordingly, web-enabled databases introduce a new tool for epidemiologists, permitting direct data capture at source and thus avoiding many of the delays and errors arising from paper forms and manual data entry. In addition, real-time data collection permits sophisticated decision support and reporting, and thus improved project co-ordination and participation. Nevertheless, the technology is complex and the development of a web-application requires an attention to information technology project management equal to that of the scientific trial or investigation. The potential and problems of web database applications are illustrated by a bespoke system ('PathMan') developed by the Veterinary Laboratories Agency of the United Kingdom Department for Environment, Food and Rural Affairs to manage a large multi-site study investigating the pathogenesis of bovine tuberculosis in England and Wales.

Animal Diseases↗

PubMed2004

Hembase: browser and genome portal for hematology and erythroid biology.

Hembase (http://hembase.niddk.nih.gov) is an integrated browser and genome portal designed for web-based examination of the human erythroid transcriptome. To date, Hembase contains 15,752 entries from erythroblast Expressed Sequenced Tags (ESTs) and 380 referenced genes relevant for erythropoiesis. The database is organized to provide a cytogenetic band position, a unique name as well as a concise annotation for each entry. Search queries may be performed by name, keyword or cytogenetic location. Search results are linked to primary sequence data and three major human genome browsers for access to information considered current at the time of each search. Hembase provides interested scientists and clinical hematologists with a genome-based approach toward the study of erythroid biology.

Computational Biology↗

PubMed2002

Using NetCloak to develop server-side Web-based experiments without writing CGI programs.

Server-side experiments use the Web server, rather than the participant's browser, to handle tasks such as random assignment, eliminating inconsistencies with JAVA and other client-side applications. Heretofore, experimenters wishing to create server-side experiments have had to write programs to create common gateway interface (CGI) scripts in programming languages such as Perl and C++. NetCloak uses simple, HTML-like commands to create CGIs. We used NetCloak to implement an experiment on probability estimation. Measurements of time on task and participants' IP addresses assisted quality control. Without prior training, in less than 1 month, we were able to use NetCloak to design and create a Web-based experiment and to help graduate students create three Web-based experiments of their own.

Internet↗

PubMed2006

Evaluation of web-based annotation of ophthalmic images for multicentric clinical trials.

An Internet browser-based annotation system can be used to identify and describe features in digitalized retinal images, in multicentric clinical trials, in real time. In this web-based annotation system, the user employs a mouse to draw and create annotations on a transparent layer, that encapsulates the observations and interpretations of a specific image. Multiple annotation layers may be overlaid on a single image. These layers may correspond to annotations by different users on the same image or annotations of a temporal sequence of images of a disease process, over a period of time. In addition, geometrical properties of annotated figures may be computed and measured. The annotations are stored in a central repository database on a server, which can be retrieved by multiple users in real time. This system facilitates objective evaluation of digital images and comparison of double-blind readings of digital photographs, with an identifiable audit trail. Annotation of ophthalmic images allowed clinically feasible and useful interpretation to track properties of an area of fundus pathology. This provided an objective method to monitor properties of pathologies over time, an essential component of multicentric clinical trials. The annotation system also allowed users to view stereoscopic images that are stereo pairs. This web-based annotation system is useful and valuable in monitoring patient care, in multicentric clinical trials, telemedicine, teaching and routine clinical settings.

Humans↗

PubMed1996

A top-down approach to whole genome visualization.

The investigation of large DNA contigs like complete chromosomes or genomes requires novel methods of data visualization. The complex information contained in a genome, particularly the relation of its individual genetic elements, needs to be accessible in a comprehensive, intelligent and intelligible manner. The yeast genome is expected to contain more than 6,000 Open Reading Frames (ORFs). As yet, the function of many of these ORFs has not been characterized satisfactorily. Also, many ORFs are found to have redundant copies elsewhere in the genome that originated from common ancestors. Other genetic elements (e.g. Tss, delta-elements, t-RNAs) are present in multiple copies. To visualize these relationships, a top-down "genome browser" is introduced that enables inspection of genomic data at different levels of abstraction (e.g. chromosomes, coding/non-coding regions, high/low levels of similarity). This novel tool is a key component for the integrated services approach to biological sequence data management (Heumann et al. 1995) and is accessible through the world wide web (WWW). This work demonstrates how the genome browser visualizes the results of an all-against-all comparison of the elements in the yeast genome as a graph. Interactive navigational queries across yeast chromosomes along the lines of sequence similarity open versatile options for the detailed investigation of genome properties. For sequence comparison the hashed position tree HPT (Mewes & Heumann 1995) is applied. Sequence similarity relationships are represented using the genome similarity graph (GSG) (Heumann & Mewes 1996c).

Chromosomes, Fungal↗

PubMed2006

TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits.

UNLABELLED: Investigators conducting studies of the molecular genetics of complex traits in humans often need rationally to select a set of single nucleotide polymorphisms (SNPs) from the hundreds or thousands available for a candidate gene. Accomplishing this requires integration of genomic data from distributed databases and is both time-consuming and error-prone. We developed the TAMAL (Technology And Money Are Limiting) web site to help identify promising SNPs for further investigation. For a given list of genes, TAMAL identifies SNPs that meet user-specified criteria (e.g. haplotype tagging SNPs or SNP predicted to lead to amino acid changes) from current versions of online resources (i.e. HapMap, Perlegen, Affymetrix, dbSNP and the UCSC genome browser). AVAILABILITY: TAMAL is a platform independent web-based application available free of charge at http://neoref.ils.unc.edu/tamal. SUPPLEMENTARY INFORMATION: http://neoref.ils.unc.edu/tamal/.

Chromosome Mapping↗