ANNIS: a linguistic database for exploring information structure

In this paper, we discuss the design and implementation of our first version of the database "ANNIS" (ANNotation of Information Structure). For research based on empirical data, ANNIS provides a uniform environment for storing this data together with its linguistic annotations. A central database promotes standardized annotation, which facilitates interpretation and comparison of the data. ANNIS is used through a standard web browser and offers tier-based visualization of data and annotations, as well as search facilities that allow for cross-level and cross-sentential queries. The paper motivates the design of the system, characterizes its user interface, and provides an initial technical evaluation of ANNIS with respect to data size and query processing

Dynamic Mashup Interfaces for Information Systems using Widgets-as-a-Service

Web Information Systems intend to adapt to the users’ preferences as new data available on the network. In this regard, the composition and reuse of services which are involved in a web application is an interesting research topic, since these techniques pursue the dynamic construction of applications that can be adapted at design or run time. As for the visualization of these applications, web user interfaces play a key role, serving as a connection point between users and the rest of the system. This article proposes an architecture for specification, storage, management and visualization of components, built from widgets complying with the W3C recommendation, for making web user interfaces. We follow a service-based approach for the interface deployment and communication management, introducing the concept of Widgets-as-a-Service (WaaS). To illustrate this proposal, an example of widget-based Web Information System is shown

Dynamic Data Extraction and Data Visualization with Application to the Kentucky Mesonet

There is a need to integrate large-scale database, high-performance computing engines and geographical information system technologies into a user-friendly web interface as a platform for data visualization and customized statistical analysis. We present some concepts and design ideas regarding dynamic data storage and extraction by making use of open-source computing and mapping technologies. We implemented our methods to the Kentucky Mesonet automated weather mapping workflow. The main components of the work flow includes a web based interface, a robust database and computing infrastructure designed for both general users and power users such as modelers and researchers

CANCERTOOL: A Visualization and Representation Interface to Exploit Cancer Datasets

[EN] With the advent of OMICs technologies, both individual research groups and consortia have spear-headed the characterization of human samples of multiple pathophysiologic origins, resulting in thousands of archived genomes and transcriptomes. Although a variety of web tools are now available to extract information from OMICs data, their utility has been limited by the capacity of nonbioinformatician researchers to exploit the information. To address this problem, we have developed CANCERTOOL, a web-based interface that aims to overcome the major limitations of public transcriptomics dataset analysis for highly prevalent types of cancer (breast, prostate, lung, and colorectal). CANCERTOOL provides rapid and comprehensive visualization of gene expression data for the gene(s) of interest in well-annotated cancer datasets. This visualization is accompanied by generation of reports customized to the interest of the researcher (e.g., editable figures, detailed statistical analyses, and access to raw data for reanalysis). It also carries out gene-to-gene correlations in multiple datasets at the same time or using preset patient groups. Finally, this new tool solves the time-consuming task of performing functional enrichment analysis with gene sets of interest using up to 11 different databases at the same time. Collectively, CANCERTOOL represents a simple and freely accessible interface to interrogate well-annotated datasets and obtain publishable representations that can contribute to refinement and guidance of cancer-related investigations at all levels of hypotheses and design. Significance: In order to facilitate access of research groups without bioinformatics support to public transcriptomics data, we have developed a free online tool with an easy-to-use interface that allows researchers to obtain quality information in a readily publishable forma

Analysis of Visualisation and Interaction Tools Authors

This document provides an in-depth analysis of visualization and interaction tools employed in the context of Virtual Museum. This analysis is required to identify and design the tools and the different components that will be part of the Common Implementation Framework (CIF). The CIF will be the base of the web-based services and tools to support the development of Virtual Museums with particular attention to online Virtual Museum.The main goal is to provide to the stakeholders and developers an useful platform to support and help them in the development of their projects, despite the nature of the project itself. The design of the Common Implementation Framework (CIF) is based on an analysis of the typical workflow ofthe V-MUST partners and their perceived limitations of current technologies. This document is based also on the results of the V-MUST technical questionnaire (presented in the Deliverable 4.1). Based on these two source of information, we have selected some important tools (mainly visualization tools) and services and we elaborate some first guidelines and ideas for the design and development of the CIF, that shall provide a technological foundation for the V-MUST Platform, together with the V-MUST repository/repositories and the additional services defined in the WP4. Two state of the art reports, one about user interface design and another one about visualization technologies have been also provided in this document

Using web GIS to promote stakeholder understanding of scientific results in sustainable urban development: A case study in Bergen, Norway

This paper highlights the importance of improving stakeholder understanding of environmental factors such as air quality and the urban heat island effect to achieve sustainable development goals. While accurate spatial and temporal environmental data are critical for sustainable solutions, the challenge lies in translating complex environmental information for non-specialists. To solve this problem, we propose using web GIS storytelling as a powerful tool for communicating and disseminating information about the environment. This paper aims to show example of implementation of a web-based geographic information system (GIS) on our case study in Bergen, Norway. This platform “Web GIS Bergen, air quality and thermal comfort” was created as an open portal. This document explains the components of the platform, their rationale, and implementation, which includes important steps. They involve the collection of relevant environmental data, including modeling results and remote sensing data. Futhermore, the design and interface of the platform has been carefully considered to provide a user-friendly experience based on interactive maps and storytelling. Combining data visualization and storytelling, the platform promotes a comprehensive understanding of complex environmental data, including “invisible killers” such as air pollution and the urban heat island effect, which significantly affect sustainable development. The strategic integration of this web-based GIS platform in Bergen can serve as an attractive model for other urban areas looking for practical tools for sustainable development, engaging stakeholders for a healthier and more sustainable urban future

Personalizovana vizuelizacija geo-informacija iz integrisanih izvora informacija zasnovana na semantici i web tehnologijama

The research subject of this PhD thesis is personalized vizuelization of geo-information originating from integrated geo-information sources, performed within Web-based Geographic Information Systems (Web GIS). The research presented in this PhD thesis includes the definition, design and implementation of Web GIS system architecture that enables personalized visualization of geospatial information based on contextual information. The presented architecture relies on the usage of GeoNis framework for interoperability of GIS applications. GeoNis platform uses a hybrid ontology approach for information integration purposes. By taking advantage of hybrid ontology approach, GeoNis platform provides an infrastructure that enables acquiring geospatial information from a large number of GIS systems, whereas GIS systems implement their interface components in the form of Web services developed according to geospatial information dissemination standards. The presented architecture enables efficient usage of GIS system’s interface components to provide customers with a personalized view over the integrated geo-information available within any of the GIS system integrated within GeoNis platform. The presented architecture of Web Geo-Information System for personalized visualization of geospatial information uses a textual description of user preferences as a baseline for selection of geospatial content from integrated geo-information sources for individual users. A description of user preferences is used to discover geo-information sources within GeoNis platform, whereby user preferences description becomes the basis for the development of user context, in terms of selected information and maps. To discover geo-information sources, described architecture takes advantage of semantic description of integrated geo-information sources, e.g. integrated GIS systems (application). As a semantic description of the integrated geospatial information sources, this process is capable of utilizing domain GeoNis ontology and local ontologies of integrated GIS systems. The model used for storing user’s contextual information within the presented Web GIS system is defined according to the OGC Web Map Context Document specification. The development of a Web GIS system according to the proposed architecture included the development of specification and implementation of a Web service that enables creating, storing and acquiring contextual documents developed for a particular user. Also, this PhD thesis included an implementation of a mechanism that allows the prediction of geospatial context of new Web GIS system user, in terms of the selection of geospatial information and maps for individual Web GIS system user. This mechanism is based on the use of metadata that had to be previously developed for each Web GI Service in the presented Web GIS system architecture. Due to the importance of a symbology used to visualize information in a GIS, an implementation of a Web GIS system for personalized visualization of integrated geospatial information included a development of a specification and implementation of the repository that enables creating, storing and acquiring symbology used to visualize geospatial information

WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations

BACKGROUND: Allele-specific (AS) Polymerase Chain Reaction is a convenient and inexpensive method for genotyping Single Nucleotide Polymorphisms (SNPs) and mutations. It is applied in many recent studies including population genetics, molecular genetics and pharmacogenomics. Using known AS primer design tools to create primers leads to cumbersome process to inexperience users since information about SNP/mutation must be acquired from public databases prior to the design. Furthermore, most of these tools do not offer the mismatch enhancement to designed primers. The available web applications do not provide user-friendly graphical input interface and intuitive visualization of their primer results. RESULTS: This work presents a web-based AS primer design application called WASP. This tool can efficiently design AS primers for human SNPs as well as mutations. To assist scientists with collecting necessary information about target polymorphisms, this tool provides a local SNP database containing over 10 million SNPs of various populations from public domain databases, namely NCBI dbSNP, HapMap and JSNP respectively. This database is tightly integrated with the tool so that users can perform the design for existing SNPs without going off the site. To guarantee specificity of AS primers, the proposed system incorporates a primer specificity enhancement technique widely used in experiment protocol. In particular, WASP makes use of different destabilizing effects by introducing one deliberate 'mismatch' at the penultimate (second to last of the 3'-end) base of AS primers to improve the resulting AS primers. Furthermore, WASP offers graphical user interface through scalable vector graphic (SVG) draw that allow users to select SNPs and graphically visualize designed primers and their conditions. CONCLUSION: WASP offers a tool for designing AS primers for both SNPs and mutations. By integrating the database for known SNPs (using gene ID or rs number), this tool facilitates the awkward process of getting flanking sequences and other related information from public SNP databases. It takes into account the underlying destabilizing effect to ensure the effectiveness of designed primers. With user-friendly SVG interface, WASP intuitively presents resulting designed primers, which assist users to export or to make further adjustment to the design. This software can be freely accessed at http://bioinfo.biotec.or.th/WASP

Metadata visualization of scholarly search results

Studies of online search behaviour have found that searchers often face difficulties formulating queries and exploring the search results sets. These shortcomings may be especially problematic in digital libraries since library searchers employ a wide variety of information-seeking methods (with varying degrees of support), and the corpus to be searched is often more complex than simple textual information. To address these problems, an interactive Web-based library search interface is presented, which has been designed to support strategic retrieval behaviour of library searchers. This system takes advantage of the rich metadata associated with academic documents and employs information visualization techniques to provide searchers with additional information-seeking tools. These tools are designed to facilitate visual and interactive query refinement, search results exploration, and citation navigation. User evaluations illustrate the potential benefits of the design choices in comparison to a list-based digital library search interface