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Scientific innovation depends on finding, integrating, and re-using the products of previous research. Here we explore how recent developments in Web technology, particularly those related to the publication of data and metadata, might assist that process by providing semantic enhancements to journal articles within the mainstream process of scholarly(More)
A workflow-centric research object bundles a workflow, the provenance of the results obtained by its enactment, other digital objects that are relevant for the experiment (papers, datasets, etc.), and annotations that semantically describe all these objects. In this paper, we propose a model to specify workflow-centric research objects, and show how the(More)
—Workflows provide a popular means for preserving scientific methods by explicitly encoding their process. However, some of them are subject to a decay in their ability to be re-executed or reproduce the same results over time, largely due to the volatility of the resources required for workflow executions. This paper provides an analysis of the root causes(More)
The Web is now being used as a platform for publishing and linking life science data. The Web's linking architecture can be exploited to join heterogeneous data from multiple sources. However, as data are frequently being updated in a decentralized environment, provenance information becomes critical to providing reliable and trustworthy services to(More)
Some of the shared digital artefacts of digital research are executable in the sense that they describe an automated process which generates results. One example is the computational scientific workflow which is used to conduct automated data analysis, predictions and validations. We describe preservation challenges of scientific workflows, and suggest a(More)
FlyTED, the Drosophila Testis Gene Expression Database, is a biological research database for gene expression images from the testis of the fruit fly Drosophila melanogaster. It currently contains 2762 mRNA in situ hybridization images and ancillary metadata revealing the patterns of gene expression of 817 Drosophila genes in testes of wild type flies and(More)
To created a linked data web of heterogeneous biological data resources, we need not only to define and create the alignment between related data resources but also to express the knowledge about why data items from different sources are linked with each other and how each data link has evolved, so that scientists can trust the data links provided by the(More)
MOTIVATION Integrating heterogeneous data across distributed sources is a major requirement for in silico bioinformatics supporting translational research. For example, genome-scale data on patterns of gene expression in the fruit fly Drosophila melanogaster are widely used in functional genomic studies in many organisms to inform candidate gene selection(More)
Research Objects (ROs) provide a exible model to collate and describe the semantic context of science. In this position paper we describe how ROs can also provide a foundation for interoperability within RESTful architecture design, enabling the development of new services and clients alongside compatible enhancements to existing software including(More)