ShareFAIR Knowledge Base – Workflow metadata
This corpus describes a collection of ontologies (EDAM, EFO, SIO), tool specifications (bio.tools), workflow repository (WorkflowHub) and workflow metadata files (RO-Crates in JSON-LD format) of open-source workflows from WorkflowHub. They are used to populate a knowlegde base of workflow
This corpus describes a collection of ontologies (EDAM, EFO, SIO), tool specifications (bio.tools), workflow repository (WorkflowHub) and workflow metadata files (RO-Crates in JSON-LD format) of open-source workflows from WorkflowHub.
They are used to populate a knowlegde base of workflow metadata, for their annotation and querying.
The file bioschemas-dump.ttl contains bio.tools data, retrieved 2025-11-23 (https://github.com/research-software-ecosystem/content/raw/refs/heads/master/datasets/bioschemas-dump.ttl).
The file EDAM.owl contains EDAM data, retrieved 2025-11-25, latest unstable version (https://edamontology.org/EDAM.owl).
WorkflowHub contents is stored in 2024-06-19-wfhub-dump.ttl (https://raw.githubusercontent.com/research-software-ecosystem/content/refs/heads/master/datasets/2024-06-19-wfhub-dump.ttl).
SIO and EFO were fetched on 2025-11-23 (https://raw.githubusercontent.com/MaastrichtU-IDS/semanticscience/refs/heads/master/ontology/sio.owl, https://raw.githubusercontent.com/EBISPOT/efo/refs/heads/master/efo-base.owl).
RO-Crate metadata files were generated with Python scripts, for CWL and Nextflow workflows extracted from WorkflowHub, and Galaxy IWC workflows.
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Files are hosted on the source repository. Click download to access the full dataset.