On 2016-01-28, Carole Goble presented Research Objects, FAIRDOM and SEEK4Science at the Dagstuhl Seminar 16041 Reproducibility of Data-Oriented Experiments in e-Science:
Making scientific experiments FAIR – findable, accessible, interoperable, reusable – is hard. To be reproducible means bundling, along with the narrative, the experimental methods, computational codes, data, algorithms, workflows, scripts – some of which might be hosted remotely, in many different repositories and with the potential to change. In this talk I presented a framework for Research Objects – a metadata framework for bundling, porting and linking resources and representing the context of experiments.
Research Objects have a manifest and a container. The manifest uses off the shelf standards and ontologies to construct the manifest and describe the content held in a container. The description is tailored to the type of Research Object, for example a Systems Biology Experiment or a computational workflow. The description broadly covers provenance, dependencies, versioning and checklists (aka reporting guidelines). Containers are off the shelf packaging platforms like Zip, Docker, Bagit or bespoke platforms that are “RO native”.
In the talk I presented FAIRDOMHub, a Systems Biology Commons for supporting the reporting and sharing of models, data and Standard Operating Procedures arising from projects. It is built on the RO-compliant SEEK4Science commons and cataloguing platform. The system gathers the metadata needed for reproducible modelling. Moreover it supports the packaging up of content to be exported and deposited into other repositories like Zenodo.
Finally I presented other implementations of the RO framework: the COMBINE Archive for Systems Biology models which uses zip, Workflow RO bundles using Bagit, which is part of the Common Workflow Language, the STELAR Asthma eLab which uses Docker and ATLAS LHC Experiments, which uses Docker and CDE.
Abstract by Carole Goble, distributed under Creative Commons Attribution 3.0 license, typographically adapted from Dagstuhl Report 16041 section 3.6 (https://doi.org/10.4230/DagRep.6.1.108) by Stian Soiland-Reyes.