An Approach to Publish Spatial Data on the Web: The GeoLinked Data Case

In this paper we report on an ongoing process aimed at publishing hydrographical data on the Web with a Spanish GeoLinked Data Use Case. Moreover, we discuss the process we followed, and propose methodological guidelines for all the activities involved within the process

The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases.

Model organisms are essential experimental platforms for discovering gene functions, defining protein and genetic networks, uncovering functional consequences of human genome variation, and for modeling human disease. For decades, researchers who use model organisms have relied on Model Organism Databases (MODs) and the Gene Ontology Consortium (GOC) for expertly curated annotations, and for access to integrated genomic and biological information obtained from the scientific literature and public data archives. Through the development and enforcement of data and semantic standards, these genome resources provide rapid access to the collected knowledge of model organisms in human readable and computation-ready formats that would otherwise require countless hours for individual researchers to assemble on their own. Since their inception, the MODs for the predominant biomedical model organisms [Mus sp (laboratory mouse), Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Danio rerio, and Rattus norvegicus] along with the GOC have operated as a network of independent, highly collaborative genome resources. In 2016, these six MODs and the GOC joined forces as the Alliance of Genome Resources (the Alliance). By implementing shared programmatic access methods and data-specific web pages with a unified "look and feel," the Alliance is tackling barriers that have limited the ability of researchers to easily compare common data types and annotations across model organisms. To adapt to the rapidly changing landscape for evaluating and funding core data resources, the Alliance is building a modern, extensible, and operationally efficient "knowledge commons" for model organisms using shared, modular infrastructure

Language technologies and the evolution of the semantic web

The availability of huge amounts of semantic markup on the Web promises to enable a quantum leap in the level of support available to Web users for locating, aggregating, sharing, interpreting and customizing information. While we cannot claim that a large scale Semantic Web already exists, a number of applications have been produced, which generate and exploit semantic markup, to provide advanced search and querying functionalities, and to allow the visualization and management of heterogeneous, distributed data. While these tools provide evidence of the feasibility and tremendous potential value of the enterprise, they all suffer from major limitations, to do primarily with the limited degree of scale and heterogeneity of the semantic data they use. Nevertheless, we argue that we are at a key point in the brief history of the Semantic Web and that the very latest demonstrators already give us a glimpse of what future applications will look like. In this paper, we describe the already visible effects of these changes by analyzing the evolution of Semantic Web tools from smart databases towards applications that harness collective intelligence. We also point out that language technology plays an important role in making this evolution sustainable and we highlight the need for improved support, especially in the area of large-scale linguistic resources

GO-WORDS: An Entropic Approach to Semantic Decomposition of Gene Ontology Terms

The Gene Ontology (GO) has a large and growing number of terms that constitute its vocabulary. An entropy-based approach is presented to automate the characterization of the compositional semantics of GO terms. The motivation is to extend the machine-readability of GO and to offer insights for the continued maintenance and growth of GO. A proto-type implementation illustrates the benefits of the approach

A review of user interface adaption in current semantic web browsers

The semantic web is an example of an innumerable corpus because it contains innumerable subjects expressed using innumerable ontologies. This paper reviews current semantic web browsers to see if they can adaptively show meaningful data presentations to users. The paper also seeks to discover if current semantic web browsers provide a rich enough set of capabilities for future user interface work to be built upon

NITELIGHT: A Graphical Tool for Semantic Query Construction

Query formulation is a key aspect of information retrieval, contributing to both the efficiency and usability of many semantic applications. A number of query languages, such as SPARQL, have been developed for the Semantic Web; however, there are, as yet, few tools to support end users with respect to the creation and editing of semantic queries. In this paper we introduce a graphical tool for semantic query construction (NITELIGHT) that is based on the SPARQL query language specification. The tool supports end users by providing a set of graphical notations that represent semantic query language constructs. This language provides a visual query language counterpart to SPARQL that we call vSPARQL. NITELIGHT also provides an interactive graphical editing environment that combines ontology navigation capabilities with graphical query visualization techniques. This paper describes the functionality and user interaction features of the NITELIGHT tool based on our work to date. We also present details of the vSPARQL constructs used to support the graphical representation of SPARQL queries

WormBase: a comprehensive resource for nematode research

WormBase (http://www.wormbase.org) is a central data repository for nematode biology. Initially created as a service to the Caenorhabditis elegans research field, WormBase has evolved into a powerful research tool in its own right. In the past 2 years, we expanded WormBase to include the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes. This comparative data enrich the C. elegans data with improved gene predictions and a better understanding of gene function. In turn, they bring the wealth of experimental knowledge of C. elegans to other systems of medical and agricultural importance. Here, we describe new species and data types now available at WormBase. In addition, we detail enhancements to our curatorial pipeline and website infrastructure to accommodate new genomes and an extensive user base