Research Object Crate for Build WorkflowHub Knowledge Graph

# 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](https://workflowhub.eu/). [](https://github.com/workflowhub-eu/workflowhub-graph/actions/workflows/push-docker.yaml) [](https://github.com/workflowhub-eu/workflowhub-graph/actions/workflows/lint-and-test.yaml) [](https://github.com/workflowhub-eu/workflowhub-graph/actions/workflows/publish-kg.yaml) ## v1.0.0 This version of the workflow was used to generate version 2025-08-29 of the WorkflowHub Knowledge Graph (https://doi.org/10.5281/zenodo.16995374). It is documented by the report "EuroScienceGateway MS6: Integrated EuroScienceGateway knowledge graph" https://doi.org/10.5281/zenodo.16992674. ## Getting Started This tool is run as a Snakemake workflow. We recommend building a Docker container to run the workflow: ```bash docker build -t knowledgegraph . ``` Then, you can run the workflow using the following command: ```bash 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: ```bash # 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](https://black.readthedocs.io/en/stable/) for code formatting. Please format your code using Black before submitting a pull request (PR) - **Type Hinting**: Please use type hints ([PEP 484](https://www.python.org/dev/peps/pep-0484/)), and docstrings ([PEP 257](https://www.python.org/dev/peps/pep-0257/)) 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](https://opensource.org/license/bsd-2-clause)

Author

Alexander Hambley, Oliver Woolland, Eli Chadwick, Volodymyr Savchenko, José Mª Fernández, Stian Soiland-Reyes

License

BSD-2-Clause

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