Consuming Linked Closed Data

The growth of the Linked Data corpus will eventually pre- vent all but the most determined of consumers from including every Linked Dataset in a single undertaking. In addition, we anticipate that the need for effective revenue models for Linked Data publishing will spur the rise of Linked Closed Data, where access to datasets is restricted. We argue that these impeding changes necessitate an overhaul of our current practices for consuming Linked Data. To this end, we propose a model for consuming Linked Data, built on the notion of continuous Information Quality assessment, which brings together a range of existing research and highlights a number of avenues for future work

A linked data approach to publishing complex scientific workflows

Past data management practices in many fields of natural science, including climate research, have focused primarily on the final research output - the research publication - with less attention paid to the chain of intermediate data results and their associated metadata, including provenance. Data were often regarded merely as an adjunct to the publication, rather than a scientific resource in their own right. In this paper, we attempt to address the issues of capturing and publishing detailed workflows associated with the climate/research datasets held by the Climatic Research Unit (CRU) at the University of East Anglia. To this end, we present a customisable approach to exposing climate research workflows for the effective re-use of the associated data, through the adoption of linked-data principles, existing widely adopted citation techniques (Digital Object Identifier) and data exchange mechanisms (Open Archives Initiative Object Reuse and Exchange)

PAV ontology: provenance, authoring and versioning

Provenance is a critical ingredient for establishing trust of published scientific content. This is true whether we are considering a data set, a computational workflow, a peer-reviewed publication or a simple scientific claim with supportive evidence. Existing vocabularies such as DC Terms and the W3C PROV-O are domain-independent and general-purpose and they allow and encourage for extensions to cover more specific needs. We identify the specific need for identifying or distinguishing between the various roles assumed by agents manipulating digital artifacts, such as author, contributor and curator. We present the Provenance, Authoring and Versioning ontology (PAV): a lightweight ontology for capturing just enough descriptions essential for tracking the provenance, authoring and versioning of web resources. We argue that such descriptions are essential for digital scientific content. PAV distinguishes between contributors, authors and curators of content and creators of representations in addition to the provenance of originating resources that have been accessed, transformed and consumed. We explore five projects (and communities) that have adopted PAV illustrating their usage through concrete examples. Moreover, we present mappings that show how PAV extends the PROV-O ontology to support broader interoperability. The authors strived to keep PAV lightweight and compact by including only those terms that have demonstrated to be pragmatically useful in existing applications, and by recommending terms from existing ontologies when plausible. We analyze and compare PAV with related approaches, namely Provenance Vocabulary, DC Terms and BIBFRAME. We identify similarities and analyze their differences with PAV, outlining strengths and weaknesses of our proposed model. We specify SKOS mappings that align PAV with DC Terms.Comment: 22 pages (incl 5 tables and 19 figures). Submitted to Journal of Biomedical Semantics 2013-04-26 (#1858276535979415). Revised article submitted 2013-08-30. Second revised article submitted 2013-10-06. Accepted 2013-10-07. Author proofs sent 2013-10-09 and 2013-10-16. Published 2013-11-22. Final version 2013-12-06. http://www.jbiomedsem.com/content/4/1/3

Enhanced Search for Educational Resources - A Perspective and a Prototype from ccLearn

Users of search tools who seek educational materials on the Internet are typically presented with either a web-scale search (e.g., Google or Yahoo) or a specialized, site-specific tool. The specialized search tools often rely upon custom data fields, such as user-entered ratings, to provide additional value. As currently designed, these systems are generally too labor intensive to manage and scale up beyond a single site or set of resources.However, custom (or structured) data of some form is necessary if search outcomes foreducational materials are to be improved. For example, design criteria and evaluative metrics are crucial attributes for educational resources, and these currently require human labeling and verification. Thus, one challenge is to design a search tool that capitalizes on available structured data (also called metadata) but is not crippled if the data are missing. This information should be amenable to repurposing by anyone, which means that it must be archived in a manner that can be discovered and leveraged easily.In this paper, we describe the extent to which DiscoverEd, a prototype developed by ccLearn, meets the design challenge of a scalable, enhanced search platform for educational resources. We then explore some of the key challenges regarding enhanced search for topic-specific Internet resources generally. We conclude by illustrating some possible future developments and third-party enhancements to the DiscoverEd prototype

Expressing the tacit knowledge of a digital library system as linked data

Library organizations have enthusiastically undertaken semantic web initiatives and in particular the data publishing as linked data. Nevertheless, different surveys report the experimental nature of initiatives and the consumer difficulty in re-using data. These barriers are a hindrance for using linked datasets, as an infrastructure that enhances the library and related information services. This paper presents an approach for encoding, as a Linked Vocabulary, the "tacit" knowledge of the information system that manages the data source. The objective is the improvement of the interpretation process of the linked data meaning of published datasets. We analyzed a digital library system, as a case study, for prototyping the "semantic data management" method, where data and its knowledge are natively managed, taking into account the linked data pillars. The ultimate objective of the semantic data management is to curate the correct consumers' interpretation of data, and to facilitate the proper re-use. The prototype defines the ontological entities representing the knowledge, of the digital library system, that is not stored in the data source, nor in the existing ontologies related to the system's semantics. Thus we present the local ontology and its matching with existing ontologies, Preservation Metadata Implementation Strategies (PREMIS) and Metadata Objects Description Schema (MODS), and we discuss linked data triples prototyped from the legacy relational database, by using the local ontology. We show how the semantic data management, can deal with the inconsistency of system data, and we conclude that a specific change in the system developer mindset, it is necessary for extracting and "codifying" the tacit knowledge, which is necessary to improve the data interpretation process

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

Using semantic indexing to improve searching performance in web archives

The sheer volume of electronic documents being published on the Web can be overwhelming for users if the searching aspect is not properly addressed. This problem is particularly acute inside archives and repositories containing large collections of web resources or, more precisely, web pages and other web objects. Using the existing search capabilities in web archives, results can be compromised because of the size of data, content heterogeneity and changes in scientific terminologies and meanings. During the course of this research, we will explore whether semantic web technologies, particularly ontology-based annotation and retrieval, could improve precision in search results in multi-disciplinary web archives

The Evolution of myExperiment

The myExperiment social website for sharing scientific workflows, designed according to Web 2.0 principles, has grown to be the largest public repository of its kind. It is distinctive for its focus on sharing methods, its researcher-centric design and its facility to aggregate content into sharable 'research objects'. This evolution of myExperiment has occurred hand in hand with its users. myExperiment now supports Linked Data as a step toward our vision of the future research environment, which we categorise here as '3rd generation e-Research'

Observing observatories: web observatories should use linked data

Web Observatories are a major international scientific collaboration concerned with data sources of a heterogeneous nature, and often quite large. Of course, they are not the first such collaboration; the Web itself was born as a response to a similar scientific endeavor. It is therefore appropriate to look at other col-laborative activities, and try to learn and use the lessons they have learnt.We argue that Web Observatories should build in interoperability using current best practices right from the start. We also argue that Linked Data is a best practice, and can provide the basis for a research environment that will deliver the vision of a large group of cooperating Observatories, sharing data and re-search results to the benefit of all. In addition, we argue that the activity should not start with a major standardization process, but should grow around appro-priate standards as required