{"id":23370181,"url":"https://github.com/maastrichtu-ids/d2s-project-template","last_synced_at":"2025-04-10T16:21:15.129Z","repository":{"id":92531530,"uuid":"200231429","full_name":"MaastrichtU-IDS/d2s-project-template","owner":"MaastrichtU-IDS","description":"📋 Template to build CWL workflows to convert data to a RDF Knowledge Graph and deploy services.","archived":false,"fork":false,"pushed_at":"2024-09-03T20:59:10.000Z","size":15263,"stargazers_count":5,"open_issues_count":9,"forks_count":0,"subscribers_count":13,"default_branch":"master","last_synced_at":"2025-03-24T14:10:29.006Z","etag":null,"topics":["cwl-workflows","knowledge-graph","rdf","sparql"],"latest_commit_sha":null,"homepage":"https://d2s.semanticscience.org/","language":"Jupyter 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Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"## Define CWL workflows for RDF conversion\n\nClick on the **Use this template** button to **create a new repository used by the [d2s Command Line Interface](https://pypi.org/project/d2s/) tool**. \n\nSee **[d2s.semanticscience.org](https://d2s.semanticscience.org/)** for detailed documentation to run CWL workflows to transform structured data to a target RDF knowledge graph and deploy services.\n\n## Requirements\n\n* [Docker](https://docs.docker.com/install/): see the [d2s Docker installation documentation](https://d2s.semanticscience.org/docs/d2s-installation#install-docker) for quick install on various systems.\n\n- `pip` install the [d2s client](https://pypi.org/project/d2s/) and [cwlref-runner](https://github.com/common-workflow-language/cwltool#install) (run workflows of Docker containers) withon Python 3.6+\n\n  ```bash\n  sudo apt install d2s cwlref-runner\n  ```\n\n## Create  a project\n\nFollow the prompt instructions to create a project in the provided folder:\n\n```bash\nd2s init project-folder-name\n```\n\n\u003e See the [d2s.semanticscience.org](https://d2s.semanticscience.org/docs/d2s-services) for the complete documentation.\n\n## Edit this template\n\nYou might want to edit or modify this template: \n\n```bash\ngit clone --recursive https://github.com/MaastrichtU-IDS/d2s-project-template.git\n```\n\n## Update submodules\n\nYou might want to update the `d2s-core` submodule to get the latest updates for the docker deployments definitions:\n\n```shell\n./update_submodules.sh\n```\n\n## About\n\nWe use the [Common Workflow Language](https://www.commonwl.org/) to describe workflows to transform heterogeneous structured data (CSV, TSV, RDB, XML, JSON) to a target RDF data model ([BioLink](https://biolink.github.io/biolink-model/docs/) in those examples). \n\nThe user can transform the input data as RDF using various solutions:\n\n* RML mappings\n* CWL workflows executing [SPARQL queries](https://github.com/MaastrichtU-IDS/d2s-project-template/blob/master/datasets/cohd/mapping/1-concepts.rq) to transform the generic RDF generated depending on the input data structure ([AutoR2RML](https://github.com/MaastrichtU-IDS/AutoR2RML), [xml2rdf](https://github.com/MaastrichtU-IDS/xml2rdf)) to the target model of his choice. See [documentation to run CWL workflows](https://d2s.semanticscience.org/docs/d2s-run)\n* [BioThings Studio](https://d2s.semanticscience.org/docs/d2s-biothings) (web UI and API)\n* DOCKET multiomics provider (Python notebooks and Nextflow)","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaastrichtu-ids%2Fd2s-project-template","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmaastrichtu-ids%2Fd2s-project-template","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaastrichtu-ids%2Fd2s-project-template/lists"}