What is RO-Crate?

https://www.researchobject.org/ro-crate/

RO-Crate is method for describing a dataset as a digital object using a single linked-data metadata document

Credit: Peter Sefton
Adapted from https://arkisto-platform.github.io/standards/ro-crate/

The dataset may contain any kind of
data resource, about anything, in any format
as a file or URL

Credit: Peter Sefton
Adapted from https://arkisto-platform.github.io/standards/ro-crate/

Each resource can have a machine readable description in JSON-LD format

Credit: Peter Sefton
Adapted from https://arkisto-platform.github.io/standards/ro-crate/

A human-readable description/preview can be in an HTML file that lives alongside the metadata

Credit: Peter Sefton
Adapted from https://arkisto-platform.github.io/standards/ro-crate/

Provenance and workflow information can be included
– to assist in re-use of data and research processes

Credit: Peter Sefton
Adapted from https://arkisto-platform.github.io/standards/ro-crate/

RO-Crate Digital Objects may be packaged for distribution eg via Zip, Bagit and OCFL
– or simply be published on the Web

Credit: Peter Sefton
Adapted from https://arkisto-platform.github.io/standards/ro-crate/

RO-Crate for
research outputs

https://doi.org/10.1016/j.future.2011.08.004

RO-Crate for data scientists

https://arkisto-platform.github.io/describo/

Credit: Marco La Rosa, Peter Sefton

Credit: Marco La Rosa, Peter Sefton
https://arkisto-platform.github.io/tools/description/describo-online/

RO-Crate for
data management plans

Credit: Tomasz Miksa et al
https://doi.org/10.4126/FRL01-006423291

Machine-actionable Data Management Plans

Use case #1: From exemplar RO-Crate generate maDMP

Use case #2: From maDMP generate template RO-Crate

RO-Crate for repositories

RO-Crate as a archival format for repositories

Metadata held alongside hetereogeneous data

Exchange mechanism (import/export)

Avoid vendor lock-in

RO-Crate for
workflow descriptions

https://about.workflowhub.eu/Workflow-RO-Crate/

https://pypi.org/project/galaxy2cwl/

Describing workflows with RO-Crate

RO-Crate for
workflow test specifications

Credit: Simone Leo

https://lifemonitor.eu/workflow_testing_ro_crate

Workflow Testing RO-Crate

• Workflow definition (e.g. Galaxy, Snakemake)
• Test suite: Instances of Test definitions
• Binds to particular test engines, e.g. Planemo, Jenkins

RO-Crate for
workflow run provenance

RO-Crate minimal provenance: Some software was used

https://www.researchobject.org/ro-crate/1.1/provenance.html

https://doi.org/10.5281/zenodo.4633732

ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data

Credit: Rudolf Wittner
https://doi.org/10.5281/zenodo.3901011

Credit: Farah Zaib Khan

https://doi.org/10.1093/gigascience/giz095

CWLProv

Credit: Thanasis Vergoulis

https://doi.org/10.5281/zenodo.4671709

https://github.com/athenarc/schema

Executing Workflow RO-Crates

Credit: José Mª Fernández, ELIXIR All Hands, 2021-06-11

https://github.com/inab/WfExS-backend/

RO-Crate for
computational tools

https://mmb.irbbarcelona.org/biobb/

https://doi.org/10.5281/zenodo.4602855

Making Canonical Workflow Building Blocks interoperable across workflow languages

RO-Crate for
data citations

Credit: Paolo Manghi
https://agu-data.github.io/DataCitationCoP/

4-dimensional RO-Crates?

Credit: Oscar Corcho, Carole Goble
https://doi.org/10.5281/zenodo.4913285