Workflow forever: Semantic Web Semantic models and tools for preserving and digitally publishing computational experiments

One of the main challenges for biomedical research lies in the integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms, for instance to explain the onset and progression of human diseases. Computer-assisted methodology is needed to perform these studies, posing new challenges for upholding scientific quality standards for the reproducibility of science. This pertains to the preservation of the 'materials and methods' of computational experiments as a record of the evidence for the biological interpretation of their results. We argue that traditional journal publication is no longer sufficient, and propose a methodology based on the workflow paradigm, Semantic Web models, and Digital Library infrastructure. Our primary goal is to enable the preservation of the necessary and sufficient information for researchers to understand the steps of a computational experiment that led to new biological insight, at any point in the future. Central to our approach is the development of a 'Research Object' (RO) model that captures this information for preservation, publication and acknowledgement. We adopted a combination of a Semantic Web and Digital Library approach for the representation and publication of such a model. The RO model can be viewed as an artifact that aggregates and annotates a number of resources that are used and/or produced in a given scientific investigation. The figure below (Figure 1) illustrates a high level description of the elements that are needed to specify a research object. Copyright © 2011 ACM.