The building and application of a semantic platform for an e-research society

Abstract

This thesis reviews the area of e-Research (the use of electronic infrastructure to support research) and considers how the insight gained from the development of social networking sites in the early 21st century might assist researchers in using this infrastructure. In particular it examines the myExperiment project, a website for e-Research that allows users to upload, share and annotate work flows and associated files, using a social networking framework. This Virtual Organisation (VO) supports many of the attributes required to allow a community of users to come together to build an e-Research society.

The main focus of the thesis is how the emerging society that is developing out of my-Experiment could use Semantic Web technologies to provide users with a significantly richer representation of their research and research processes to better support reproducible research. One of the initial major contributions was building an ontology for myExperiment. Through this it became possible to build an API for generating and delivering this richer representation and an interface for querying it.

Having this richer representation it has been possible to follow Linked Data principles to link up with other projects that have this type of representation. Doing this has allowed additional data to be provided to the user and has begun to set in context the data produced by myExperiment. The way that the myExperiment project has gone about this task and consideration of how changes may affect existing users, is another major contribution of this thesis.

Adding a semantic representation to an emergent e-Research society like myExperiment,has given it the potential to provide additional applications. In particular the capability to support Research Objects, an encapsulation of a scientist's research or research process to support reproducibility. The insight gained by adding a semantic representation to myExperiment, has allowed this thesis to contribute towards the design of the architecture for these Research Objects that use similar Semantic Web technologies.

The myExperiment ontology has been designed such that it can be aligned with other ontologies. Scientific Discourse, the collaborative argumentation of different claims and hypotheses, with the support of evidence from experiments, to construct, confirm or disprove theories requires the capability to represent experiments carried out in silico. This thesis discusses how, as part of the HCLS Scientific Discourse subtask group, the myExperiment ontology has begun to be aligned with other scientific discourse ontologies to provide this capability. It also compares this alignment of ontologies with the architecture for Research Objects.

This thesis has also examines how myExperiment's Linked Data and that of other projects can be used in the design of novel interfaces. As a theoretical exercise, it considers how this Linked Data might be used to support a Question-Answering system, that would allow users to query myExperiment's data in a more efficient and user-friendly way.

It concludes by reviewing all the steps undertaken to provide a semantic platform for an emergent e-Research society to facilitate the sharing of research and its processes to support reproducible research. It assesses their contribution to enhancing the features provided by myExperiment, as well as e-Research as a whole. It considers how the contributions provided by this thesis could be extended to produce additional tools that will allow researchers to make greater use of the rich data that is now available, in a way that enhances their research process rather than significantly changing it or adding extra workload.

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Identifiers

ORCID for David R. Newman: orcid.org/0000-0001-5153-5396

ORCID for David De Roure: orcid.org/0000-0001-9074-3016

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