Corresponding authors: Paul De Geest (
Academic editor:
We introduce how the Galaxy research environment (
RO-Crate (
The RO-Crate community brings together practitioners from very different backgrounds, and with different motivations and use cases. Among the core target users are:
researchers engaged with computation and data-intensive, workflow-driven analysis; digital repository managers and infrastructure providers; individual researchers looking for a straightforward tool or how-to guide to “FAIRify” their data; data stewards supporting research projects in creating and curating datasets.
Given the wide applicability of RO-Crate and the lack of practical implementations of FDOs, ELIXIR (
Tools have been developed towards aiding the previously mentioned use cases and increasing the general usability of RO-Crates by providing a user-friendly (programmatic) interface for consumption and production of RO-Crates through programmatic libraries for consuming/producing RO-Crates (ro-crate-py
The Galaxy project provides a research environment with data analysis and data management functionalities as a multi user platform, aiming to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. As such, it stores not just analysis related data but also the complete analytical workflow, including its metadata. The internal data model involves the history entity, including all steps performed in a specific analysis, and the workflow entity, defining the structure of an analytical pipeline. From the start, Galaxy aims to enable reproducible analyses by providing capabilities to export (and import) all the analysis history details and workflow data and metadata in a FAIR way. As such it helps its users with the daily research data management. The Galaxy community is continuously improving and adding features, the integration of the FAIR Digital Object principles is a natural next step in this.
To be able to support these FDOs, Galaxy leverages the RO-Crate Python client library (
a workflow definition, which is used to share/publish the details of an analysis pipeline, including the graph of tools that need to be executed, and metadata about the data types required individual data files or a collection of datasets related to an analysis history a compressed archive of the entire analysis history including the metadata associated with it such as the tools used, their versions, the parameters chosen, workflow invocation related metadata, inputs, outputs, license, author, CWLProv description (
The adoption of RO-crate by Galaxy allows a standardised exchange of FDOs with other platforms in the ELIXIR Tools ecosystem, such as WorkflowHub and LifeMonitor. Integrating RO-Crate deeply into Galaxy and offering import and export options of various Galaxy objects such as Research Objects allows for increased standardisation, improved Research Data Management (RDM) functionalities, smoother user experience (UX) as well as improved interoperability with other systems. The integration in a platform used by biologists to do data intensive analysis, facilitates the publication of workflows and workflow invocations for all skill levels and democratises the ability to perform Open Science.
Paul De Geest
First International Conference on FAIR Digital Objects, poster