WorkflowHub Knowledge Graph

A tool to generate a knowledge graph from a source of RO Crates. By default, this tool sources and generates an RDF graph of crates from WorkflowHub.

Getting Started

This tool is run as a Snakemake workflow. We recommend building a Docker container to run the workflow:

docker build -t knowledgegraph .

Then, you can run the workflow using the following command:

docker run --rm -v ./workflow-output:/app/output --user $(id -u):$(id -g) knowledgegraph

Where ./workflow-output is the directory where the output will be stored (already created for you in this repo) and the --user flag ensures that the output files are created with the correct permissions.

Structure

• source_ro_crates: This rule sources RO crates from the WorkflowHub API (source_crates.py)
• create_graph: This rule merges the individual RO crates into a single RDF graph
• enrich_graph: This rule processes the base graph and adds additional metadata from external sources e.g. WikiData, Orcid
• merge_graphs: This rule merges the base graph and enrichment graphs
• consolidate: This rule collapses duplicate entries around canonical objects to make the graph easier to navigate

[!TIP]

This diagram is generated with:

docker run --entrypoint '' knowledgegraph snakemake --dag | dot -Tsvg > docs/images/dag.svg

Visualisation / exploration

Bundled in this repo is a stack which allows the knowledge graph to be explored visually and interactively.

The containers in the stack provide:

• A triplestore to make SPARQL queries against
• A visualisation tool
• A one-shot tool to configure the visualisation tool

To view the visualisation run:

# run the workflow as above
cd vis
docker compose down -v # clears configuration, skip if first run, refine if confident with Docker
docker compose up
# View visualisation on localhost:4200

Contributing

Coding Style

• Code Formatting: We use Python Black for code formatting. Please format your code using Black before submitting a pull request (PR)
• Type Hinting: Please use type hints (PEP 484), and docstrings (PEP 257) in methods and classes.

Branching Strategy

• Branch Naming: When working on a new feature or bug fix, create a branch from develop. e.g. feature/description or bugfix/description.
• Development Branch: The develop branch is currently our main integration branch. Features and fixes should target develop through PRs.
• Feature Branches: These feature branches should be short-lived and focused. Once done, please create a pull request to merge it into develop.

License

BSD 2-Clause License