Will this work for Susan? Challenges for delivering usable and useful generic linked data browsers

While we witness an explosion of exploration tools for simple datasets on Web 2.0 designed for use by ordinary citizens, the goal of a usable interface for supporting navigation and sense-making over arbitrary linked data has remained elusive. The purpose of this paper is to analyse why - what makes exploring linked data so hard? Through a user-centered use case scenario, we work through requirements for sense making with data to extract functional requirements and to compare these against our tools to see what challenges emerge to deliver a useful, usable knowledge building experience with linked data. We present presentation layer and heterogeneous data integration challenges and offer practical considerations for moving forward to effective linked data sensemaking tools

Internet based molecular collaborative and publishing tools

The scientific electronic publishing model has hitherto been an Internet based delivery of electronic articles that are essentially replicas of their paper counterparts. They contain little in the way of added semantics that may better expose the science, assist the peer review process and facilitate follow on collaborations, even though the enabling technologies have been around for some time and are mature. This thesis will examine the evolution of chemical electronic publishing over the past 15 years. It will illustrate, which the help of two frameworks, how publishers should be exploiting technologies to improve the semantics of chemical journal articles, namely their value added features and relationships with other chemical resources on the Web. The first framework is an early exemplar of structured and scalable electronic publishing where a Web content management system and a molecular database are integrated. It employs a test bed of articles from several RSC journals and supporting molecular coordinate and connectivity information. The value of converting 3D molecular expressions in chemical file formats, such as the MOL file, into more generic 3D graphics formats, such as Web3D, is assessed. This exemplar highlights the use of metadata management for bidirectional hyperlink maintenance in electronic publishing. The second framework repurposes this metadata management concept into a Semantic Web application called SemanticEye. SemanticEye demonstrates how relationships between chemical electronic articles and other chemical resources are established. It adapts the successful semantic model used for digital music metadata management by popular applications such as iTunes. Globally unique identifiers enable relationships to be established between articles and other resources on the Web and SemanticEye implements two: the Document Object Identifier (DOI) for articles and the IUPAC International Chemical Identifier (InChI) for molecules. SemanticEye’s potential as a framework for seeding collaborations between researchers, who have hitherto never met, is explored using FOAF, the friend-of-a-friend Semantic Web standard for social networks

The building and application of a semantic platform for an e-research society

This thesis reviews the area of e-Research (the use of electronic infrastructure to support research) and considers how the insight gained from the development of social networking sites in the early 21st century might assist researchers in using this infrastructure. In particular it examines the myExperiment project, a website for e-Research that allows users to upload, share and annotate work flows and associated files, using a social networking framework. This Virtual Organisation (VO) supports many of the attributes required to allow a community of users to come together to build an e-Research society. The main focus of the thesis is how the emerging society that is developing out of my-Experiment could use Semantic Web technologies to provide users with a significantly richer representation of their research and research processes to better support reproducible research. One of the initial major contributions was building an ontology for myExperiment. Through this it became possible to build an API for generating and delivering this richer representation and an interface for querying it. Having this richer representation it has been possible to follow Linked Data principles to link up with other projects that have this type of representation. Doing this has allowed additional data to be provided to the user and has begun to set in context the data produced by myExperiment. The way that the myExperiment project has gone about this task and consideration of how changes may affect existing users, is another major contribution of this thesis. Adding a semantic representation to an emergent e-Research society like myExperiment,has given it the potential to provide additional applications. In particular the capability to support Research Objects, an encapsulation of a scientist's research or research process to support reproducibility. The insight gained by adding a semantic representation to myExperiment, has allowed this thesis to contribute towards the design of the architecture for these Research Objects that use similar Semantic Web technologies. The myExperiment ontology has been designed such that it can be aligned with other ontologies. Scientific Discourse, the collaborative argumentation of different claims and hypotheses, with the support of evidence from experiments, to construct, confirm or disprove theories requires the capability to represent experiments carried out in silico. This thesis discusses how, as part of the HCLS Scientific Discourse subtask group, the myExperiment ontology has begun to be aligned with other scientific discourse ontologies to provide this capability. It also compares this alignment of ontologies with the architecture for Research Objects. This thesis has also examines how myExperiment's Linked Data and that of other projects can be used in the design of novel interfaces. As a theoretical exercise, it considers how this Linked Data might be used to support a Question-Answering system, that would allow users to query myExperiment's data in a more efficient and user-friendly way. It concludes by reviewing all the steps undertaken to provide a semantic platform for an emergent e-Research society to facilitate the sharing of research and its processes to support reproducible research. It assesses their contribution to enhancing the features provided by myExperiment, as well as e-Research as a whole. It considers how the contributions provided by this thesis could be extended to produce additional tools that will allow researchers to make greater use of the rich data that is now available, in a way that enhances their research process rather than significantly changing it or adding extra workload

Building a semantic blog support system for gene Learning Objects on Web 2.0 environment / by Wei Yuan.

Blogging has become a popular practice on Internet in recent years, and it has been used as information publishing and participate platforms. In recent years, a style of blog called 'semantic blogs' have been introduced into the field. Semantic blogs are blogs enriched with machine-understandable metadata (Mller, Breslin, & Decker, 2005). They are an extension of regular blogs. Recently, a new web technology theory was proposed called Web 2.0. Unlike traditional web technology which only allows web users to accept information passively, Web 2.0 provides web users the option to actively modify web information. Learning Objects are digital entities deliverable over the Internet. Any number of people can access and use them simultaneously. Moreover, users can collaborate on learning objects and benefit immediately from adding their information or appending others' work to Learning Objects and share with other users over the Internet. This thesis is dedicated to the development of a semantic blog prototype for Gene Ontology annotation and navigation as a Web 2.0 support system. We are developing this semantic blog specifically because we did not find an effective system already in place that can provide support for biomedical researchers. The existing Gene Ontology systems can be classified into various categories: offline applications, client-server applications, web search engines, portals, and FTP servers. Researchers face a number of bottlenecks within the current system; all of them are based on traditional web technology with no collaboration among individual gene ontology researchers, and annotation can only be published by certain organizations. This thesis seeks the possibility to use Learning Object with Gene Ontology along with the semantic of how researchers collaborate as represented by FOAF. We have therefore introduced a new Gene ontology Annotation and navigation System. Colloquially referred to as GAS, it is based on Web 2.0 technologies with extended semantic capabilities that include Gene Ontology semantics, SCORM semantics, FOAF semantics, RSS syndication, aggregation semantics, as well as a useful and important gene ontology and annotation navigation system - Gene Ontology Navigation (GON). Our evaluation of the GAS prototype has proven to be extremely effective

A widget library for creating policy-aware semantic Web applications

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2010.Cataloged from PDF version of thesis.Includes bibliographical references (p. 79-81).In order to truly reap the benefits of the Semantic Web, there must be adequate tools for writing Web applications that aggregate, view, and edit the widely varying data the Semantic Web makes available. As a step toward this goal, I introduce a Javascript widget library for creating Web applications that can both read from and write to the Semantic Web. In addition to providing widgets that perform editing operations, access control rules for user-generated content are supported using FOAF+SSL, a decentralized authentication technique, allowing for users to independently manage the restrictions placed on their data. I demonstrate this functionality with two examples: an aggregator application for exploring information about musicians from multiple data stores, and a universal annotation widget that allows users to make public and private comments about any resource on the Semantic Web.by James Dylan Hollenbach.M.Eng

Data DNA: The Next Generation of Statistical Metadata

Describes the components of a complete statistical metadata system and suggests ways to create and structure metadata for better access and understanding of data sets by diverse users

Approaches to visualising linked data: a survey

The uptake and consumption of Linked Data is currently restricted almost entirely to the Semantic Web community. While the utility of Linked Data to non-tech savvy web users is evident, the lack of technical knowledge and an understanding of the intricacies of the semantic technology stack limit such users in their ability to interpret and make use of the Web of Data. A key solution in overcoming this hurdle is to visualise Linked Data in a coherent and legible manner, allowing non-domain and non-technical audiences to obtain a good understanding of its structure, and therefore implicitly compose queries, identify links between resources and intuitively discover new pieces of information. In this paper we describe key requirements which the visualisation of Linked Data must fulfil in order to lower the technical barrier and make the Web of Data accessible for all. We provide an extensive survey of current efforts in the Semantic Web community with respect to our requirements, and identify the potential for visual support to lead to more effective, intuitive interaction of the end user with Linked Data. We conclude with the conclusions drawn from our survey and analysis, and present proposals for advancing current Linked Data visualisation efforts

GI Systems for public health with an ontology based approach

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.Health is an indispensable attribute of human life. In modern age, utilizing technologies for health is one of the emergent concepts in several applied fields. Computer science, (geographic) information systems are some of the interdisciplinary fields which motivates this thesis. Inspiring idea of the study is originated from a rhetorical disease DbHd: Database Hugging Disorder, defined by Hans Rosling at World Bank Open Data speech in May 2010. The cure of this disease can be offered as linked open data, which contains ontologies for health science, diseases, genes, drugs, GEO species etc. LOD-Linked Open Data provides the systematic application of information by publishing and connecting structured data on the Web. In the context of this study we aimed to reduce boundaries between semantic web and geo web. For this reason a use case data is studied from Valencia CSISP- Research Center of Public Health in which the mortality rates for particular diseases are represented spatio-temporally. Use case data is divided into three conceptual domains (health, spatial, statistical), enhanced with semantic relations and descriptions by following Linked Data Principles. Finally in order to convey complex health-related information, we offer an infrastructure integrating geo web and semantic web. Based on the established outcome, user access methods are introduced and future researches/studies are outlined