Web-based Search Tool Research Articles

Traveler Information Tool with Integrated Real-Time Transit Information and Multimodal Trip Planning

The chief objective of the PATH2Go multimodal traveler information application is to improve the accessibility and the quality of real-time traveler information and to make transit a known and viable choice for travelers. PATH2Go was developed as part of a field test on the US-101 corridor in the San Francisco Bay Area of California, with the primary hypothesis that travelers would benefit from real-time multimodal traveler information and therefore would be likely to consider using transit. PATH2Go integrates a web-based multimodal trip-planning tool that uses real-time transit, traffic, and parking information; a web-based search tool that finds real-time information about transit arrivals and schedules; and a mobile application that provides personalized en route transit trip information. PATH2Go integrates these major components of traveler information in one platform and makes real-time information easily accessible to travelers. The PATH2Go system architecture and major design considerations are described, and enabling technologies–including the Global Positioning System (GPS) fusing algorithm and a scenario-parsing algorithm based on GPS location data–are introduced.

ZFIN: enhancements and updates to the zebrafish model organism database

ZFIN, the Zebrafish Model Organism Database, http://zfin.org, serves as the central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. ZFIN manually curates comprehensive data for zebrafish genes, phenotypes, genotypes, gene expression, antibodies, anatomical structures and publications. A wide-ranging collection of web-based search forms and tools facilitates access to integrated views of these data promoting analysis and scientific discovery. Data represented in ZFIN are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations. ZFIN is a dynamic resource with data added daily as part of our ongoing curation process. Software updates are frequent. Here, we describe recent additions to ZFIN including (i) enhanced access to images, (ii) genomic features, (iii) genome browser, (iv) transcripts, (v) antibodies and (vi) a community wiki for protocols and antibodies.

FASTR3D: a fast and accurate search tool for similar RNA 3D structures

FASTR3D is a web-based search tool that allows the user to fast and accurately search the PDB database for structurally similar RNAs. Currently, it allows the user to input three types of queries: (i) a PDB code of an RNA tertiary structure (default), optionally with specified residue range, (ii) an RNA secondary structure, optionally with primary sequence, in the dot-bracket notation and (iii) an RNA primary sequence in the FASTA format. In addition, the user can run FASTR3D with specifying additional filtering options: (i) the released date of RNA structures in the PDB database, and (ii) the experimental methods used to determine RNA structures and their least resolutions. In the output page, FASTR3D will show the user-queried RNA molecule, as well as user-specified options, followed by a detailed list of identified structurally similar RNAs. Particularly, when queried with RNA tertiary structures, FASTR3D provides a graphical display to show the structural superposition of the query structure and each of identified structures. FASTR3D is now available online at http://bioalgorithm.life.nctu.edu.tw/FASTR3D/.

Teaching With Technology

In this bimonthly series, the author examines how nurse educators can use Internet and Web-based computer technologies such as search, communication, and collaborative writing tools; social networking and social bookmarking sites; virtual worlds; and Web-based teaching and learning programs. This article describes approaches to finding information on the Web. Web-based search tools including Internet search engines, organizational databases, and those at the library will be discussed. Techniques to evaluate the validity, usefulness, and applicability of search outcomes are included.

Teaching With Technology

In this bimonthly series, the author examines how nurse educators can use Internet and Web-based computer technologies such as search, communication, and collaborative writing tools, social networking and social bookmarking sites, virtual worlds, and Web-based teaching and learning programs. This article describes approaches to finding information on the Web. Web-based search tools including Internet search engines, organizational databases, and those at the library will be discussed. Techniques to evaluate the validity, usefulness, and applicability of search outcomes are included.

Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics

Nematode.net (http://nematode.net) is a publicly available resource dedicated to the study of parasitic nematodes. In 2000, the Genome Center at Washington University (GC) joined a consortium including the Nematode Genomics group in Edinburgh, and the Pathogen Sequencing Unit of the Sanger Institute to generate expressed sequence tags (ESTs) as an inexpensive and efficient solution for gene discovery in parasitic nematodes. As of 2008 the GC, sampling key parasites of humans, animals and plants, has generated over 500 000 ESTs and 1.2 million genome survey sequences from more than 30 non-Caenorhabditis elegans nematodes. Nematode.net was implemented to offer user-friendly access to data produced by this project. In addition to sequence data, the site hosts: assembled NemaGene clusters in GBrowse views characterizing composition and protein homology, functional Gene Ontology annotations presented via the AmiGO browser, KEGG-based graphical display of NemaGene clusters mapped to metabolic pathways, codon usage tables, NemFam protein families which represent conserved nematode-restricted coding sequences not found in public protein databases, a web-based WU-BLAST search tool that allows complex querying and other assorted resources. The primary aim of Nematode.net is the dissemination of this diverse collection of information to the broader scientific community in a way that is useful, consistent, centralized and enduring.

A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics research

BackgroundFor omics experiments, detailed characterisation of experimental material with respect to its genetic features, its cultivation history and its treatment history is a requirement for analyses by bioinformatics tools and for publication needs. Furthermore, meta-analysis of several experiments in systems biology based approaches make it necessary to store this information in a standardised manner, preferentially in relational databases. In the Golm Plant Database System, we devised a data management system based on a classical Laboratory Information Management System combined with web-based user interfaces for data entry and retrieval to collect this information in an academic environment.ResultsThe database system contains modules representing the genetic features of the germplasm, the experimental conditions and the sampling details. In the germplasm module, genetically identical lines of biological material are generated by defined workflows, starting with the import workflow, followed by further workflows like genetic modification (transformation), vegetative or sexual reproduction. The latter workflows link lines and thus create pedigrees. For experiments, plant objects are generated from plant lines and united in so-called cultures, to which the cultivation conditions are linked. Materials and methods for each cultivation step are stored in a separate ACCESS database of the plant cultivation unit. For all cultures and thus every plant object, each cultivation site and the culture's arrival time at a site are logged by a barcode-scanner based system. Thus, for each plant object, all site-related parameters, e.g. automatically logged climate data, are available. These life history data and genetic information for the plant objects are linked to analytical results by the sampling module, which links sample components to plant object identifiers. This workflow uses controlled vocabulary for organs and treatments. Unique names generated by the system and barcode labels facilitate identification and management of the material. Web pages are provided as user interfaces to facilitate maintaining the system in an environment with many desktop computers and a rapidly changing user community. Web based search tools are the basis for joint use of the material by all researchers of the institute.ConclusionThe Golm Plant Database system, which is based on a relational database, collects the genetic and environmental information on plant material during its production or experimental use at the Max-Planck-Institute of Molecular Plant Physiology. It thus provides information according to the MIAME standard for the component 'Sample' in a highly standardised format. The Plant Database system thus facilitates collaborative work and allows efficient queries in data analysis for systems biology research.

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms

MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and is publicly available as a web-based data resource. This paper presents the first release of a web-based search tool to explore enzyme reaction mechanisms in MACiE. We also present Version 2 of MACiE, which doubles the dataset available (from Version 1). MACiE can be accessed from

Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function

BackgroundThe purpose of this study is to determine whether or not there exists nonrandom grouping of cis-regulatory elements within gene promoters that can be perceived independent of gene expression data and whether or not there is any correlation between this grouping and the biological function of the gene.ResultsUsing ProSpector, a web-based promoter search and annotation tool, we have applied an unbiased approach to analyze the transcription factor binding site frequencies of 1400 base pair genomic segments positioned at 1200 base pairs upstream and 200 base pairs downstream of the transcriptional start site of 7298 commonly studied human genes. Partitional clustering of the transcription factor binding site composition within these promoter segments reveals a small number of gene groups that are selectively enriched for gene ontology terms consistent with distinct aspects of cellular function. Significance ranking of the class-determining transcription factor binding sites within these clusters show substantial overlap between the gene ontology terms of the transcriptions factors associated with the binding sites and the gene ontology terms of the regulated genes within each group.ConclusionThus, gene sorting by promoter composition alone produces partitions in which the "regulated" and the "regulators" cosegregate into similar functional classes. These findings demonstrate that the transcription factor binding site composition is non-randomly distributed between gene promoters in a manner that reflects and partially defines general gene class function.

Web-mapping Applications for Accessing Library Collections: Case Studies using ESRI’s ArcIMS at the National Library of Scotland

For several decades, map libraries and our users have appreciated the value of graphical search methods, and the integrating power of geographical coordinates for spatial searching (Van de Waal, 1974; Larsgaard, 1978). More recently there have been developments in software and data availability to allow the more widespread practical implementation of web-based graphical search tools, using dynamic maps and geo-referenced records. This year, the National Library of Scotland (NLS) has implemented pilot web-based applications using ESRI’s ArcIMS software, to provide an online spatial search method for NLS collections. This paper describes the background to these applications, the software and hardware used, interfaces developed, and I will end with an examination of the problems and prospects of this web-mapping technology.

Enhancing Virtual Product Representations for Advanced Design Repository Systems

This paper describes the transformation of an existing set of heterogeneous product knowledge into a coherent design repository that supports product design knowledge archival and web-based search, display, and design model and tool generation. Guided by design theory, existing product information was analyzed and compared against desired outputs to ascertain what information management structure was needed to produce design resources pertinent to the design process. Several test products were catalogued to determine what information was essential without being redundant in representation. This set allowed for the creation of a novel single point of entry application for product information and the development of a relational database for design knowledge archival. Web services were then implemented to support design knowledge retrieval through search, browse, and real-time design tool generation. Further explored in this paper are the fundamental enabling technologies of the design repository system. Additionally, repository-generated design tools are scrutinized alongside human-generated design tools for validation. Through this process researchers have been able to improve the way in which artifact data are gathered, archived, distributed and used.

A query-based approach in Web search instruction: An assessment of current practice

An instruction program that covers search tools on the Web should incorporate a user's information need as the basis for teaching these tools. This article lays the theoretical groundwork for such a query-based approach, deriving its argument from the literature published in the early days of databases in libraries. A review of recent literature as well as tutorials on the Web reveals that librarians do not routinely consider a user's query in their training in the use of Web-based search tools. Other training elements are more prevalent, in particular the nature of search tools, search strategies and the evaluation of results found in a search. When training recommends a context for searching the Web, the advice tends to be of a general nature. These results suggest that librarians may not routinely be teaching queries as a strategy for selecting and using search tools on the Web. Suggestions for further research are presented to explore these findings.

Drug rings database with web interface. A tool for identifying alternative chemical rings in lead discovery programs.

This paper describes the development of a drug rings database and Web-based search tools. The database contains ring structures from both corporate and commercial databases, along with characteristic descriptors including frequency of occurrence as an indicator of synthetic accessibility and calculated property and geometric parameters. Analysis of the rings in several major databases is described, with illustrations of applications of the database in lead discovery programs where bioisosteres and geometric isosteres are sought.