21,980 research outputs found

    The ABC ontology and model

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    This paper describes the latest version of the ABC metadata model. This model has been developed within the Harmony international digital library project to provide a common conceptual model to facilitate interoperability between metadata vocabularies from different domains. This updated ABC model is the result of collaboration with the CIMI consortium whereby earlier versions of the ABC model were applied to metadata descriptions of complex objects provided by CIMI museums and libraries. The result is a metadata model with more logically grounded time and entity semantics. Based on this model we have been able to build a metadata repository of RDF descriptions and a search interface which is capable of more sophisticated queries than less-expressive, object-centric metadata models will allow

    Towards a core ontology for information integration

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    In this paper, we argue that a core ontology is one of the key building blocks necessary to enable the scalable assimilation of information from diverse sources. A complete and extensible ontology that expresses the basic concepts that are common across a variety of domains and can provide the basis for specialization into domain-specific concepts and vocabularies, is essential for well-defined mappings between domain-specific knowledge representations (i.e., metadata vocabularies) and the subsequent building of a variety of services such as cross-domain searching, browsing, data mining and knowledge extraction. This paper describes the results of a series of three workshops held in 2001 and 2002 which brought together representatives from the cultural heritage and digital library communities with the goal of harmonizing their knowledge perspectives and producing a core ontology. The knowledge perspectives of these two communities were represented by the CIDOC/CRM [31], an ontology for information exchange in the cultural heritage and museum community, and the ABC ontology [33], a model for the exchange and integration of digital library information. This paper describes the mediation process between these two different knowledge biases and the results of this mediation - the harmonization of the ABC and CIDOC/CRM ontologies, which we believe may provide a useful basis for information integration in the wider scope of the involved communities

    Adaptive response of neonatal sepsis-derived Group B Streptococcus to bilirubin

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    This work was funded by the Neonatal Unit Endowment Fund, Aberdeen Maternity Hospital. RH is funded by a career researcher fellowship from NHS Research Scotland. SG was funded by the MRC Flagship PhD programme. We are grateful for the support of Dr Phil Cash and Aberdeen Proteomics, at University of Aberdeen, in completing this project. Supplementary information accompanies this paper at https://doi.org/10.1038/s41598-018-24811-3.Peer reviewedPublisher PD

    Analysis of the olive fruit fly Bactrocera oleae transcriptome and phylogenetic classification of the major detoxification gene families

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    he olive fruit fly Bactrocera oleae has a unique ability to cope with olive flesh, and is the most destructive pest of olives worldwide. Its control has been largely based on the use of chemical insecticides, however, the selection of insecticide resistance against several insecticides has evolved. The study of detoxification mechanisms, which allow the olive fruit fly to defend against insecticides, and/or phytotoxins possibly present in the mesocarp, has been hampered by the lack of genomic information in this species. In the NCBI database less than 1,000 nucleotide sequences have been deposited, with less than 10 detoxification gene homologues in total. We used 454 pyrosequencing to produce, for the first time, a large transcriptome dataset for B. oleae. A total of 482,790 reads were assembled into 14,204 contigs. More than 60% of those contigs (8,630) were larger than 500 base pairs, and almost half of them matched with genes of the order of the Diptera. Analysis of the Gene Ontology (GO) distribution of unique contigs, suggests that, compared to other insects, the assembly is broadly representative for the B. oleae transcriptome. Furthermore, the transcriptome was found to contain 55 P450, 43 GST-, 15 CCE- and 18 ABC transporter-genes. Several of those detoxification genes, may putatively be involved in the ability of the olive fruit fly to deal with xenobiotics, such as plant phytotoxins and insecticides. In summary, our study has generated new data and genomic resources, which will substantially facilitate molecular studies in B. oleae, including elucidation of detoxification mechanisms of xenobiotic, as well as other important aspects of olive fruit fly biology

    Distributed XQuery

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    XQuery is increasingly being used for ad-hoc integration of heterogeneous data sources that are logically mapped to XML. For example, scientists need to query multiple scientific databases, which are distributed over a large geographic area, and it is possible to use XQuery for that. However, the language currently supports only the data shipping query evaluation model (through the document() function): it fetches all data sources to a single server, then runs the query there. This is a major limitation for many applications, especially when some data sources are very large, or when a data source is only a virtual XML view over some other logical data model. We propose here a simple extension to XQuery that allows query shipping to be expressed in the language, in addition to data shipping

    Developing an ontological sandbox : investigating multi-level modelling’s possible Metaphysical Structures

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    One of the central concerns of the multi-level modelling (MLM) community is the hierarchy of classifications that appear in conceptual models; what these are, how they are linked and how they should be organised into levels and modelled. Though there has been significant work done in this area, we believe that it could be enhanced by introducing a systematic way to investigate the ontological nature and requirements that underlie the frameworks and tools proposed by the community to support MLM (such as Orthogonal Classification Architecture and Melanee). In this paper, we introduce a key component for the investigation and understanding of the ontological requirements, an ontological sandbox. This is a conceptual framework for investigating and comparing multiple variations of possible ontologies – without having to commit to any of them – isolated from a full commitment to any foundational ontology. We discuss the sandbox framework as well as walking through an example of how it can be used to investigate a simple ontology. The example, despite its simplicity, illustrates how the constructional approach can help to expose and explain the metaphysical structures used in ontologies, and so reveal the underlying nature of MLM levelling

    Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq

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    Background: The European red mite, Panonychus ulmi, is among the most important mite pests in fruit orchards, where it is controlled primarily by acaricide application. However, the species rapidly develops pesticide resistance, and the elucidation of resistance mechanisms for P. ulmi has not kept pace with insects or with the closely related spider mite Tetranychus urticae. The main reason for this lack of knowledge has been the absence of genomic resources needed to investigate the molecular biology of resistance mechanisms. Results: Here, we provide a comprehensive strand-specific RNA-seq based transcriptome resource for P. ulmi derived from strains susceptible and resistant to the widely used acaricide spirodiclofen. From a de novo assembly of the P. ulmi transcriptome, we manually annotated detoxification enzyme families, target-sites of commonly used acaricides, and horizontally transferred genes implicated in plant-mite interactions and pesticide resistance. In a comparative analysis that incorporated sequences available for Panonychus citri, T. urticae, and insects, we identified radiations for detoxification gene families following the divergence of Panonychus and Tetranychus genera. Finally, we used the replicated RNA-seq data from the spirodiclofen susceptible and resistant strains to describe gene expression changes associated with resistance. A cytochrome P450 monooxygenase, as well as multiple carboxylcholinesterases, were differentially expressed between the susceptible and resistant strains, and provide a molecular entry point for understanding resistance to spirodiclofen, widely used to control P. ulmi populations. Conclusions: The new genomic resources and data that we present in this study for P. ulmi will substantially facilitate molecular studies of underlying mechanisms involved in acaricide resistance

    Synote: weaving media fragments and linked data

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    While end users could easily share and tag the multimedia resources online, the searching and reusing of the inside content of multimedia, such as a certain area within an image or a ten minutes segment within a one-hour video, is still difficult. Linked data is a promising way to interlink media fragments with other resources. Many applications in Web 2.0 have generated large amount of external annotations linked to media fragments. In this paper, we use Synote as the target application to discuss how media fragments could be published together with external annotations following linked data principles. Our design solves the dereferencing, describing and interlinking methods problems in interlinking multimedia. We also implement a model to let Google index media fragments which improves media fragments' online presence. The evaluation shows that our design can successfully publish media fragments and annotations for both semantic Web agents and traditional search engines. Publishing media fragments using the design we describe in this paper will lead to better indexing of multimedia resources and their consequent findabilit
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