51,307 research outputs found

    The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web

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    Research in life sciences is increasingly being conducted in a digital and online environment. In particular, life scientists have been pioneers in embracing new computational tools to conduct their investigations. To support the sharing of digital objects produced during such research investigations, we have witnessed in the last few years the emergence of specialized repositories, e.g., DataVerse and FigShare. Such repositories provide users with the means to share and publish datasets that were used or generated in research investigations. While these repositories have proven their usefulness, interpreting and reusing evidence for most research results is a challenging task. Additional contextual descriptions are needed to understand how those results were generated and/or the circumstances under which they were concluded. Because of this, scientists are calling for models that go beyond the publication of datasets to systematically capture the life cycle of scientific investigations and provide a single entry point to access the information about the hypothesis investigated, the datasets used, the experiments carried out, the results of the experiments, the people involved in the research, etc. In this paper we present the Research Object (RO) suite of ontologies, which provide a structured container to encapsulate research data and methods along with essential metadata descriptions. Research Objects are portable units that enable the sharing, preservation, interpretation and reuse of research investigation results. The ontologies we present have been designed in the light of requirements that we gathered from life scientists. They have been built upon existing popular vocabularies to facilitate interoperability. Furthermore, we have developed tools to support the creation and sharing of Research Objects, thereby promoting and facilitating their adoption.Comment: 20 page

    Graph-based discovery of ontology change patterns

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    Ontologies can support a variety of purposes, ranging from capturing conceptual knowledge to the organisation of digital content and information. However, information systems are always subject to change and ontology change management can pose challenges. We investigate ontology change representation and discovery of change patterns. Ontology changes are formalised as graph-based change logs. We use attributed graphs, which are typed over a generic graph with node and edge attribution.We analyse ontology change logs, represented as graphs, and identify frequent change sequences. Such sequences are applied as a reference in order to discover reusable, often domain-specific and usagedriven change patterns. We describe the pattern discovery algorithms and measure their performance using experimental result

    National Center for Biomedical Ontology: Advancing biomedicine through structured organization of scientific knowledge

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    The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease

    A Process Framework for Semantics-aware Tourism Information Systems

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    The growing sophistication of user requirements in tourism due to the advent of new technologies such as the Semantic Web and mobile computing has imposed new possibilities for improved intelligence in Tourism Information Systems (TIS). Traditional software engineering and web engineering approaches cannot suffice, hence the need to find new product development approaches that would sufficiently enable the next generation of TIS. The next generation of TIS are expected among other things to: enable semantics-based information processing, exhibit natural language capabilities, facilitate inter-organization exchange of information in a seamless way, and evolve proactively in tandem with dynamic user requirements. In this paper, a product development approach called Product Line for Ontology-based Semantics-Aware Tourism Information Systems (PLOSATIS) which is a novel hybridization of software product line engineering, and Semantic Web engineering concepts is proposed. PLOSATIS is presented as potentially effective, predictable and amenable to software process improvement initiatives

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

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    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

    Automatic detection of accommodation steps as an indicator of knowledge maturing

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    Jointly working on shared digital artifacts – such as wikis – is a well-tried method of developing knowledge collectively within a group or organization. Our assumption is that such knowledge maturing is an accommodation process that can be measured by taking the writing process itself into account. This paper describes the development of a tool that detects accommodation automatically with the help of machine learning algorithms. We applied a software framework for task detection to the automatic identification of accommodation processes within a wiki. To set up the learning algorithms and test its performance, we conducted an empirical study, in which participants had to contribute to a wiki and, at the same time, identify their own tasks. Two domain experts evaluated the participants’ micro-tasks with regard to accommodation. We then applied an ontology-based task detection approach that identified accommodation with a rate of 79.12%. The potential use of our tool for measuring knowledge maturing online is discussed
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