sheeba-samuel / reopen

ReOpen (Reopen for Reproducibility)

This work presents the REPRODUCE-ME ontology which is used to describe the scientific experiments and is extended from the W3C vocabulary PROV-O and P-Plan. It is used to represent the whole picture of a scientific experiment describing the path it took from its design to result with the aim to enable end-to-end reproducibility. The ontology describes the activities, entities, agents, steps, plans, variables, locations and time that are related to an experiment. This ontology is developed taking microscopy experiments as an example. It also describes the properties of a microscopic image and its acquisition using the OME data model. The ontology is extended to describe the provenance of Jupyter Notebook execution in a multi-user environment provided by JupyterHub. The ontology is used and evaluated in the prototype "ReOpen". The prototype is based on a provenance-based semantic approach where scientists get a overall view of the experiments from the experiment material preparation step to the results generated by scripts in JupyterHub. The example Jupyter Notebooks used for evaluating the prototype can be found here.

This work is supported by the Deutsche Forschungsgemeinschaft (DFG) in Project Z2 of the CRC/TRR 166 High-end light microscopy elucidates membrane receptor function - ReceptorLight.

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