6,487 research outputs found
Ontology-based knowledge representation of experiment metadata in biological data mining
According to the PubMed resource from the U.S. National Library of Medicine,
over 750,000 scientific articles have been published in the ~5000 biomedical journals
worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes
The Semantic Grid: A future e-Science infrastructure
e-Science offers a promising vision of how computer and communication technology can support and enhance the scientific process. It does this by enabling scientists to generate, analyse, share and discuss their insights, experiments and results in an effective manner. The underlying computer infrastructure that provides these facilities is commonly referred to as the Grid. At this time, there are a number of grid applications being developed and there is a whole raft of computer technologies that provide fragments of the necessary functionality. However there is currently a major gap between these endeavours and the vision of e-Science in which there is a high degree of easy-to-use and seamless automation and in which there are flexible collaborations and computations on a global scale. To bridge this practiceâaspiration divide, this paper presents a research agenda whose aim is to move from the current state of the art in e-Science infrastructure, to the future infrastructure that is needed to support the full richness of the e-Science vision. Here the future e-Science research infrastructure is termed the Semantic Grid (Semantic Grid to Grid is meant to connote a similar relationship to the one that exists between the Semantic Web and the Web). In particular, we present a conceptual architecture for the Semantic Grid. This architecture adopts a service-oriented perspective in which distinct stakeholders in the scientific process, represented as software agents, provide services to one another, under various service level agreements, in various forms of marketplace. We then focus predominantly on the issues concerned with the way that knowledge is acquired and used in such environments since we believe this is the key differentiator between current grid endeavours and those envisioned for the Semantic Grid
The Knowledge Life Cycle for e-learning
In this paper, we examine the semantic aspects of e-learning from both pedagogical and technological points of view. We suggest that if semantics are to fulfil their potential in the learning domain then a paradigm shift in perspective is necessary, from information-based content delivery to knowledge-based collaborative learning services. We propose a semantics driven Knowledge Life Cycle that characterises the key phases in managing semantics and knowledge, show how this can be applied to the learning domain and demonstrate the value of semantics via an example of knowledge reuse in learning assessment management
Methodological considerations concerning manual annotation of musical audio in function of algorithm development
In research on musical audio-mining, annotated music databases are needed which allow the development of computational tools that extract from the musical audiostream the kind of high-level content that users can deal with in Music Information Retrieval (MIR) contexts. The notion of musical content, and therefore the notion of annotation, is ill-defined, however, both in the syntactic and semantic sense. As a consequence, annotation has been approached from a variety of perspectives (but mainly linguistic-symbolic oriented), and a general methodology is lacking. This paper is a step towards the definition of a general framework for manual annotation of musical audio in function of a computational approach to musical audio-mining that is based on algorithms that learn from annotated data. 1
An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights
With an unprecedented growth in the biomedical literature, keeping up to date with
the new developments presents an immense challenge. Publications are often studied
in isolation of the established literature, with interpretation being subjective and
often introducing human bias. With ontology-driven annotation of biomedical data
gaining popularity in recent years and online databases offering metatags with rich
textual information, it is now possible to automatically text-mine ontological terms
and complement the laborious task of manual management, interpretation, and
analysis of the accumulated literature with downstream statistical analysis. In this
paper, we have formulated an automated workflow through which we have identified
ontological information, including nutrition-related terms in PubMed abstracts
(from 1991 to 2016) for two main types of Inflammatory Bowel Diseases: Crohnâs
Disease and Ulcerative Colitis; and two other gastrointestinal (GI) diseases, namely,
Coeliac Disease and Irritable Bowel Syndrome. Our analysis reveals unique clustering
patterns as well as spatial and temporal trends inherent to the considered GI diseases
in terms of literature that has been accumulated so far. Although automated
interpretation cannot replace human judgement, the developed workflow shows
promising results and can be a useful tool in systematic literature reviews. The
workflow is available at https://github.com/KociOrges/pytag
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