West
Patrick
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Toward cyberinfrastructure to facilitate collaboration and reproducibility for marine integrated ecosystem assessments
Experiences of a “semantics smackdown”
West
Patrick
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Preprint
There is a growing need for cyberinfrastructure to support science-based decision making in management of natural resources. In particular, our motivation was to aid the development of cyberinfrastructure for Integrated Ecosystem Assessments (IEAs) for marine ecosystems. The IEA process involves analysis of natural and socio-economic information based on diverse and disparate sources of data, requiring collaboration among scientists of many disciplines and communication with other stakeholders. Here we describe our bottom-up approach to developing cyberinfrastructure through a collaborative process engaging a small group of domain and computer scientists and software engineers. We report on a use case evaluated for an Ecosystem Status Report, a multi-disciplinary report inclusive of Earth, life, and social sciences, for the Northeast U.S. Continental Shelf Large Marine Ecosystem. Ultimately, we focused on sharing workflows as a component of the cyberinfrastructure to facilitate collaboration and reproducibility. We developed and deployed a software environment to generate a portion of the Report, retaining traceability of derived datasets including indicators of climate forcing, physical pressures, and ecosystem states. Our solution for sharing workflows and delivering reproducible documents includes IPython (now Jupyter) Notebooks. We describe technical and social challenges that we encountered in the use case and the importance of training to aid the adoption of best practices and new technologies by domain scientists. We consider the larger challenges for developing end-to-end cyberinfrastructure that engages other participants and stakeholders in the IEA process.
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Preprint
Within the field of ocean science there is a long history of using controlled vocabularies and other Semantic Web techniques to provide a common and easily exchanged description of datasets. As an activity within the European Union, United States, Australian-funded project “Ocean Data Interoperability Platform”, a workshop took place in June 2014 at Rensselaer Polytechnic Institute to further the use of these Semantic Web techniques with the aim of producing a set of Linked Data publication patterns which describe many parts of a marine science dataset. During the workshop, a Semantic Web development methodology was followed which promoted the use of a team with mixed skills (computer, data and marine science experts) to rapidly prototype a Linked Data publication pattern which could be iterated in the future. In this paper we outline the methodology employed in the workshop, and examine both the technical and sociological outcomes of a workshop of this kind.