Knowledge Organization Systems (KOS) in the Semantic Web: A Multi-Dimensional Review

Since the Simple Knowledge Organization System (SKOS) specification and its SKOS eXtension for Labels (SKOS-XL) became formal W3C recommendations in 2009 a significant number of conventional knowledge organization systems (KOS) (including thesauri, classification schemes, name authorities, and lists of codes and terms, produced before the arrival of the ontology-wave) have made their journeys to join the Semantic Web mainstream. This paper uses "LOD KOS" as an umbrella term to refer to all of the value vocabularies and lightweight ontologies within the Semantic Web framework. The paper provides an overview of what the LOD KOS movement has brought to various communities and users. These are not limited to the colonies of the value vocabulary constructors and providers, nor the catalogers and indexers who have a long history of applying the vocabularies to their products. The LOD dataset producers and LOD service providers, the information architects and interface designers, and researchers in sciences and humanities, are also direct beneficiaries of LOD KOS. The paper examines a set of the collected cases (experimental or in real applications) and aims to find the usages of LOD KOS in order to share the practices and ideas among communities and users. Through the viewpoints of a number of different user groups, the functions of LOD KOS are examined from multiple dimensions. This paper focuses on the LOD dataset producers, vocabulary producers, and researchers (as end-users of KOS).Comment: 31 pages, 12 figures, accepted paper in International Journal on Digital Librarie

Constitute: The world’s constitutions to read, search, and compare

Constitutional design and redesign is constant. Over the last 200 years, countries have replaced their constitutions an average of every 19 years and some have amended them almost yearly. A basic problem in the drafting of these documents is the search and analysis of model text deployed in other jurisdictions. Traditionally, this process has been ad hoc and the results suboptimal. As a result, drafters generally lack systematic information about the institutional options and choices available to them. In order to address this informational need, the investigators developed a web application, Constitute [online at http://www.constituteproject.org], with the use of semantic technologies. Constitute provides searchable access to the world’s constitutions using the conceptualization, texts, and data developed by the Comparative Constitutions Project. An OWL ontology represents 330 ‘‘topics’’ – e.g. right to health – with which the investigators have tagged relevant provisions of nearly all constitutions in force as of September of 2013. The tagged texts were then converted to an RDF representation using R2RML mappings and Capsenta’s Ultrawrap. The portal implements semantic search features to allow constitutional drafters to read, search, and compare the world’s constitutions. The goal of the project is to improve the efficiency and systemization of constitutional design and, thus, to support the independence and self-reliance of constitutional drafters.Governmen

Interoperability and FAIRness through a novel combination of Web technologies

Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved atthe level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs

Towards linked open gene mutations data

<p>Abstract</p> <p>Background</p> <p>With the advent of high-throughput technologies, a great wealth of variation data is being produced. Such information may constitute the basis for correlation analyses between genotypes and phenotypes and, in the future, for personalized medicine. Several databases on gene variation exist, but this kind of information is still scarce in the Semantic Web framework.</p> <p>In this paper, we discuss issues related to the integration of mutation data in the Linked Open Data infrastructure, part of the Semantic Web framework. We present the development of a mapping from the IARC TP53 Mutation database to RDF and the implementation of servers publishing this data.</p> <p>Methods</p> <p>A version of the IARC TP53 Mutation database implemented in a relational database was used as first test set. Automatic mappings to RDF were first created by using D2RQ and later manually refined by introducing concepts and properties from domain vocabularies and ontologies, as well as links to Linked Open Data implementations of various systems of biomedical interest.</p> <p>Since D2RQ query performances are lower than those that can be achieved by using an RDF archive, generated data was also loaded into a dedicated system based on tools from the Jena software suite.</p> <p>Results</p> <p>We have implemented a D2RQ Server for TP53 mutation data, providing data on a subset of the IARC database, including gene variations, somatic mutations, and bibliographic references. The server allows to browse the RDF graph by using links both between classes and to external systems. An alternative interface offers improved performances for SPARQL queries. The resulting data can be explored by using any Semantic Web browser or application.</p> <p>Conclusions</p> <p>This has been the first case of a mutation database exposed as Linked Data. A revised version of our prototype, including further concepts and IARC TP53 Mutation database data sets, is under development.</p> <p>The publication of variation information as Linked Data opens new perspectives: the exploitation of SPARQL searches on mutation data and other biological databases may support data retrieval which is presently not possible. Moreover, reasoning on integrated variation data may support discoveries towards personalized medicine.</p