RO-Crate: Capturing FAIR research outputs in bioinformatics and beyond

Presentation from the eScience Lab (The University of Manchester) at the ISMB/ECCB 2025 conference (view all).

RO-Crate is presented in the BOSC & BOKR track as a Flash talk: Tuesday 22 July, 15:20, room 03A. It is also presented as a Poster: A-118, Monday 21 July, 10:00-11:20 and 16:00-16:40 (viewable Mon and Tue). View video presentation on YouTube.

RO-Crate: Capturing FAIR research outputs in bioinformatics and beyond

• Source code: https://github.com/ResearchObject/ro-crate
• Website: https://www.researchobject.org/ro-crate/
• License: Apache 2.0 - https://github.com/ResearchObject/ro-crate?tab=Apache-2.0-1-ov-file#readme

Main Text of Abstract

RO-Crate is a mechanism for packaging research outputs with structured metadata, providing machine-readability and reproducibility following the FAIR principles (Findable, Accessible, Interoperable, Reusable). It enables interlinking methods, data, and outputs with the outcomes of a project or a piece of work, even where distributed across repositories.

Researchers can distribute their work as an RO-Crate to ensure their data travels with its metadata, so that key components are correctly tracked, archived, and attributed. Data stewards and infrastructure providers can integrate RO-Crate into the projects and platforms they support, to make it easier for researchers to create and consume RO-Crates without requiring technical expertise.

RO-Crate is flexible enough to support many applications and domains. It can:

• Contain files and link to large datasets stored online
• Record an entire analysis, including inputs, outputs, and tools used
• Connect related publications and datasets
• Preserve datasets for long-term archiving
• Combine multiple uses to fit different needs

Community-developed extensions called “profiles” also allow the creation of more specialised RO-Crates, describing for example workflows, data provenance, or domain-specific data formats.

Some of the current uses of RO-Crate in bioinformatics are:

• Describing computational workflows registered with the WorkflowHub platform (example)
• Creating FAIR exports of workflow executions - for example, the BioDT (Biodiversity Digital Twin) project exports workflow executions from simulations of wild relatives of crops as RO-Crates (source code). RO-Crate export is also supported by workflow engines including Galaxy, Nextflow, WfExS, CWL, and more (example)
• Enabling an appropriate level of credit and attribution, particularly in currently under-recognised roles (eg. sample gathering, processing, sample distribution)
• The DataPLANT project captures plant science experiments as Annotated Research Contexts (ARC), complex objects based on RO-Crate which describe workflows, workflow executions, inputs, and results (example)
• The Biodiversity Genomics Europe project is defining conventions for biodiversity genomics metadata as an RO-Crate profile (in development), as well as creating exports of genomics data as RO-Crates in the COPO platform

The RO-Crate specification is developed on GitHub by an open global community membership. Tools which implement the specification and profiles which extend it are also community-developed and open-source. There are also regular community calls and regional drop-ins, which will be highlighted as a good place for follow-up conversations after ISMB/BOSC.

A simple example RO-Crate can be found as a walkthrough in the introduction to the RO-Crate specification. Other examples are linked from the use cases listed above.