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PubMed2006

Chemical structure indexing of toxicity data on the internet: moving toward a flat world.

Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives that are accelerating the pace of this transformation, with particular reference to toxicology-related chemical information. Chemical content annotators, structure locator services, large structure/data aggregator web sites, structure browsers, International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) codes, toxicity data models and public chemical/biological activity profiling initiatives are all playing a role in overcoming barriers to the integration of toxicity data, and are bringing researchers closer to the reality of a mineable chemical Semantic Web. An example of this integration of data is provided by the collaboration among researchers involved with the Distributed Structure-Searchable Toxicity (DSSTox) project, the Carcinogenic Potency Project, projects at the National Cancer Institute and the PubChem database.

Abstracting and Indexing↗
PubMed2002

Planning and implementing image delivery to outpatient specialty clinical practices in a large medical center.

Softcopy image viewing using web-based technologies has been deployed to 3 specialty outpatient practices - Lung Center, Neurosurgery, Orthopedic Surgery - where films remain available. Physicians and staff use Philips Easyweb (a web-based image browser) and BJC HealthCare ClinDesk (a Java-based electronic patient record) clients in patient examination rooms and physician workrooms to retrieve images from a Mitra image server. Practice-specific planning and training preceded deployment; on-site training and support came with deployment; on-site and telephone support are available as needed. Softcopy viewing generally is accepted although a few physicians continue to use films. The unavailability of studies performed before the introduction of the image server remains an issue until the server builds a suitable archive. Softcopy-based clinical-image viewing can be supported with web-based technologies, but effective practice-specific planning, training, and technical support are crucial to successful deployment to those accepting softcopy image viewing.

Data Display↗
PubMed2005

Genomic resources for chicken.

The recent sequencing and draft assembly of a chicken genome has provided biologists with an invaluable research tool that complements a growing list of additional avian genomic resources. For many researchers, finding and using these resources is challenging, because information is presented through an increasing number of Web sites and browser navigation frequently requires specific knowledge and expertise. This primer provides an overview of online genomic resources for the chicken, including the Ensembl, UCSC, and NCBI annotated chicken genome browsers; expressed sequence tag and in situ hybridization databases; and sources for microarrays, cDNAs, and bacterial artificial chromosomes (BACs). Several short tutorials oriented toward the biologist with limited bioinformatics skills outline how to retrieve several types of commonly needed information and reagents.

Animals↗
PubMed2024

Haplotype-resolved genome assembly and implementation of VitExpress, an open interactive transcriptomic platform for grapevine.

Haplotype-resolved genome assemblies were produced for Chasselas and Ugni Blanc, two heterozygous Vitis vinifera cultivars by combining high-fidelity long-read sequencing and high-throughput chromosome conformation capture (Hi-C). The telomere-to-telomere full coverage of the chromosomes allowed us to assemble separately the two haplo-genomes of both cultivars and revealed structural variations between the two haplotypes of a given cultivar. The deletions/insertions, inversions, translocations, and duplications provide insight into the evolutionary history and parental relationship among grape varieties. Integration of de novo single long-read sequencing of full-length transcript isoforms (Iso-Seq) yielded a highly improved genome annotation. Given its higher contiguity, and the robustness of the IsoSeq-based annotation, the Chasselas assembly meets the standard to become the annotated reference genome for V. vinifera. Building on these resources, we developed VitExpress, an open interactive transcriptomic platform, that provides a genome browser and integrated web tools for expression profiling, and a set of statistical tools (StatTools) for the identification of highly correlated genes. Implementation of the correlation finder tool for MybA1, a major regulator of the anthocyanin pathway, identified candidate genes associated with anthocyanin metabolism, whose expression patterns were experimentally validated as discriminating between black and white grapes. These resources and innovative tools for mining genome-related data are anticipated to foster advances in several areas of grapevine research.

Vitis↗
PubMed2003

Documenting nursing practice by using ICNP on the Web.

This paper presents the design and implementation of an internet based nursing care planning system which helps nursing professionals and students to study ICNP beta 2 version and to create nursing diagnoses, interventions and outcomes by selecting relevant terms from ICNP. This advanced web-based ICNP browser enables the authentication of the user, and the creation of a type of nursing care plan through the use of ICNP. It provides different ways for creating nursing diagnoses, interventions and outcomes, by selecting relevant ICNP terms through the tree-structure view, index and search components of the tool. The created diagnoses, interventions and outcomes are stored to a secured database. The system provides to the user the facility to build and manage nursing care plans by using both the English and the translated Greek ICNP versions. The first results of the implementation of this internet based nursing care planning system are presented.

Database Management Systems↗
PubMed2004

Evaluating an ICNP Web-based nursing documentation system.

The purpose of this paper is to present the evaluation of a web based nursing documentation system which helps nursing professionals and students to study ICNP Greek beta 2 version and to create nursing diagnoses, interventions and outcomes by selecting relevant terms from ICNP. This advanced web-based ICNP browser enables the authentication of the user, and the creation of a type of nursing care plan through the use of ICNP. It provides different ways for creating nursing diagnoses, interventions and outcomes, by selecting relevant ICNP terms through the tree-structure view, index and search components of the tool. The evaluation of this nursing documentation system is carried out by a survey among nursing professionals working in nursing units in hospitals. The results which have derived from this survey are presented. Moreover, conclusions regarding the future changes that should be made in the system are reported.

Attitude to Computers↗
PubMed2002

The generic genome browser: a building block for a model organism system database.

The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org.

Animals↗
PubMed1999

Transparent image access in a distributed picture archiving and communications system: the Master Database broker.

A distributed design is the most cost-effective system for small-to medium-scale picture archiving and communications systems (PACS) implementations. However, the design presents an interesting challenge to developers and implementers: to make stored image data, distributed throughout the PACS network, appear to be centralized with a single access point for users. A key component for the distributed system is a central or master database, containing all the studies that have been scanned into the PACS. Each study includes a list of one or more locations for that particular dataset so that applications can easily find it. Non-Digital Imaging and Communications in Medicine (DICOM) clients, such as our worldwide web (WWW)-based PACS browser, query the master database directly to find the images, then jump to the most appropriate location via a distributed web-based viewing system. The Master Database Broker provides DICOM clients with the same functionality by translating DICOM queries to master database searches and distributing retrieval requests transparently to the appropriate source. The Broker also acts as a storage service class provider, allowing users to store selected image subsets and reformatted images with the original study, without having to know on which server the original data are stored.

CD-ROM↗
PubMed2002

The Cadmio XML healthcare record.

The management of clinical data is a complex task. Patient related information reported in patient folders is a set of heterogeneous and structured data accessed by different users having different goals (in local or geographical networks). XML language provides a mechanism for describing, manipulating, and visualising structured data in web-based applications. XML ensures that the structured data is managed in a uniform and transparent manner independently from the applications and their providers guaranteeing some interoperability. Extracting data from the healthcare record and structuring them according to XML makes the data available through browsers. The MIC/MIE model (Medical Information Category/Medical Information Elements), which allows the definition and management of healthcare records and used in CADMIO, a HISA based project, is described in this paper, using XML for allowing the data to be visualised through web browsers.

Italy↗
PubMed2004

A web server for performing electronic PCR.

'Electronic PCR' (e-PCR) refers to a computational procedure that is used to search DNA sequences for sequence tagged sites (STSs), each of which is defined by a pair of primer sequences and an expected PCR product size. To gain speed, our implementation extracts short 'words' from the 3' end of each primer and stores them in a sorted hash table that can be accessed efficiently during the search. One recent improvement is the use of overlapping discontinuous words to allow matches to be found despite the presence of a mismatch. Moreover, it is possible to allow gaps in the alignment between the primer and the sequence. The effect of these changes is to improve sensitivity without significantly affecting specificity. The new software provides a search mode using a query STS against a sequence database to augment the previously available mode using a query sequence against an STS database. Finally, e-PCR may now be used through a web service, with search results linked to other web resources such as the UniSTS database and the MapViewer genome browser. The e-PCR web server may be found at www.ncbi.nlm.nih.gov/sutils/e-pcr.

Algorithms↗
PubMed2003

The UCSC Genome Browser Database.

The University of California Santa Cruz (UCSC) Genome Browser Database is an up to date source for genome sequence data integrated with a large collection of related annotations. The database is optimized to support fast interactive performance with the web-based UCSC Genome Browser, a tool built on top of the database for rapid visualization and querying of the data at many levels. The annotations for a given genome are displayed in the browser as a series of tracks aligned with the genomic sequence. Sequence data and annotations may also be viewed in a text-based tabular format or downloaded as tab-delimited flat files. The Genome Browser Database, browsing tools and downloadable data files can all be found on the UCSC Genome Bioinformatics website (http://genome.ucsc.edu), which also contains links to documentation and related technical information.

Animals↗
PubMed2006

A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila.

BACKGROUND: Biological processes are mediated by networks of interacting genes and proteins. Efforts to map and understand these networks are resulting in the proliferation of interaction data derived from both experimental and computational techniques for a number of organisms. The volume of this data combined with the variety of specific forms it can take has created a need for comprehensive databases that include all of the available data sets, and for exploration tools to facilitate data integration and analysis. One powerful paradigm for the navigation and analysis of interaction data is an interaction graph or map that represents proteins or genes as nodes linked by interactions. Several programs have been developed for graphical representation and analysis of interaction data, yet there remains a need for alternative programs that can provide casual users with rapid easy access to many existing and emerging data sets. DESCRIPTION: Here we describe a comprehensive database of Drosophila gene and protein interactions collected from a variety of sources, including low and high throughput screens, genetic interactions, and computational predictions. We also present a program for exploring multiple interaction data sets and for combining data from different sources. The program, referred to as the Interaction Map (IM) Browser, is a web-based application for searching and visualizing interaction data stored in a relational database system. Use of the application requires no downloads and minimal user configuration or training, thereby enabling rapid initial access to interaction data. IM Browser was designed to readily accommodate and integrate new types of interaction data as it becomes available. Moreover, all information associated with interaction measurements or predictions and the genes or proteins involved are accessible to the user. This allows combined searches and analyses based on either common or technique-specific attributes. The data can be visualized as an editable graph and all or part of the data can be downloaded for further analysis with other tools for specific applications. The database is available at http://proteome.wayne.edu/PIMdb.html CONCLUSION: The Drosophila Interactions Database described here places a variety of disparate data into one easily accessible location. The database has a simple structure that maintains all relevant information about how each interaction was determined. The IM Browser provides easy, complete access to this database and could readily be used to publish other sets of interaction data. By providing access to all of the available information from a variety of data types, the program will also facilitate advanced computational analyses.

Database Management Systems↗
PubMed2003

Uzilla: a new tool for web usability testing.

Web usability testing and research presents challenges for accurate data collection. An instrumented browser solution, Uzilla, is compared with existing solutions, and its contributions to usability testing practice are noted. Uzilla implements a client-server architecture based on the open source Mozilla browser. Instrumentation of the browser facilitates the evaluation of Web sites and applications inside and outside of the laboratory. An integrated data collection and analysis server application decreases the effort required to understand test results and facilitates iterative testing.

Ergonomics↗
PubMedDate not supplied

Ophthalmology's interaction with the Internet (you say, 'Internet what?').

1. You can be connected to the information Highway by a local phone call. So, you will have a monthly charge for your access, but not a more expensive phone bill. 2. Mail lists are discussion groups; actually, they are "computer remailers." When you join a mail list, your e-mail address is entered into a computer, along with a group of people with common interest on the Net. 3. The World Wide Web is the graphical and multimedia part of the Internet--color, sound, video, and all! To access the World Wide Web, you'll need a browser. A browser is a piece of software that allows you to look at all the Web's various home pages and websites. Organizations, individuals, universities, and corporations have Web addresses (called URLs) that allow you to look at their "roadside stand" on this Information Highway.

Computer Communication Networks↗
PubMed2007

HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update.

HbVar (http://globin.bx.psu.edu/hbvar) is a locus-specific database (LSDB) developed in 2001 by a multi-center academic effort to provide timely information on the genomic sequence changes leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records include extensive phenotypic descriptions, biochemical and hematological effects, associated pathology, and ethnic occurrence, accompanied by mutation frequencies and references. In addition to the regular updates to entries, we report significant advances and updates, which can be useful not only for HbVar users but also for other LSDB development and curation in general. The query page provides more functionality but in a simpler, more user-friendly format and known single nucleotide polymorphisms in the human alpha- and beta-globin loci are provided automatically. Population-specific beta-thalassemia mutation frequencies for 31 population groups have been added and/or modified and the previously reported delta- and alpha-thalassemia mutation frequency data from 10 population groups have also been incorporated. In addition, an independent flat-file database, named XPRbase (http://www.goldenhelix.org/xprbase), has been developed and linked to the main HbVar web page to provide a succinct listing of 51 experimental protocols available for globin gene mutation screening. These updates significantly augment the database profile and quality of information provided, which should increase the already high impact of the HbVar database, while its combination with the UCSC powerful genome browser and the ITHANET web portal paves the way for drawing connections of clinical importance, that is from genome to function to phenotype.

DNA Mutational Analysis↗
PubMed2001

The ARKdb: genome databases for farmed and other animals.

The ARKdb genome databases provide comprehensive public repositories for genome mapping data from farmed species and other animals (http://www.thearkdb.org) providing a resource similar in function to that offered by GDB or MGD for human or mouse genome mapping data, respectively. Because we have attempted to build a generic mapping database, the system has wide utility, particularly for those species for which development of a specific resource would be prohibitive. The ARKdb genome database model has been implemented for 10 species to date. These are pig, chicken, sheep, cattle, horse, deer, tilapia, cat, turkey and salmon. Access to the ARKdb databases is effected via the World Wide Web using the ARKdb browser and Anubis map viewer. The information stored includes details of loci, maps, experimental methods and the source references. Links to other information sources such as PubMed and EMBL/GenBank are provided. Responsibility for data entry and curation is shared amongst scientists active in genome research in the species of interest. Mirror sites in the United States are maintained in addition to the central genome server at Roslin.

Animals↗
PubMed2006

Sealife: a semantic grid browser for the life sciences applied to the study of infectious diseases.

The objective of Sealife is the conception and realisation of a semantic Grid browser for the life sciences, which will link the existing Web to the currently emerging eScience infrastructure. The SeaLife Browser will allow users to automatically link a host of Web servers and Web/Grid services to the Web content he/she is visiting. This will be accomplished using eScience's growing number of Web/Grid Services and its XML-based standards and ontologies. The browser will identify terms in the pages being browsed through the background knowledge held in ontologies. Through the use of Semantic Hyperlinks, which link identified ontology terms to servers and services, the SeaLife Browser will offer a new dimension of context-based information integration. In this paper, we give an overview over the different components of the browser and their interplay. This SeaLife Browser will be demonstrated within three application scenarios in evidence-based medicine, literature & patent mining, and molecular biology, all relating to the study of infectious diseases. The three applications vertically integrate the molecule/cell, the tissue/organ and the patient/population level by covering the analysis of high-throughput screening data for endocytosis (the molecular entry pathway into the cell), the expression of proteins in the spatial context of tissue and organs, and a high-level library on infectious diseases designed for clinicians and their patients. For more information see http://www.biote.ctu-dresden.de/sealife.

Biological Science Disciplines↗