https://github.com/maastrichtu-ids/d2s-project-template
📋 Template to build CWL workflows to convert data to a RDF Knowledge Graph and deploy services.
https://github.com/maastrichtu-ids/d2s-project-template
cwl-workflows knowledge-graph rdf sparql
Last synced: about 2 months ago
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📋 Template to build CWL workflows to convert data to a RDF Knowledge Graph and deploy services.
- Host: GitHub
- URL: https://github.com/maastrichtu-ids/d2s-project-template
- Owner: MaastrichtU-IDS
- License: mit
- Created: 2019-08-02T12:32:40.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2024-09-03T20:59:10.000Z (9 months ago)
- Last Synced: 2025-03-24T14:10:29.006Z (2 months ago)
- Topics: cwl-workflows, knowledge-graph, rdf, sparql
- Language: Jupyter Notebook
- Homepage: https://d2s.semanticscience.org/
- Size: 14.6 MB
- Stars: 5
- Watchers: 13
- Forks: 0
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
## Define CWL workflows for RDF conversion
Click on the **Use this template** button to **create a new repository used by the [d2s Command Line Interface](https://pypi.org/project/d2s/) tool**.
See **[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.
## Requirements
* [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.
- `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+
```bash
sudo apt install d2s cwlref-runner
```
## Create a project
Follow the prompt instructions to create a project in the provided folder:
```bash
d2s init project-folder-name
```
> See the [d2s.semanticscience.org](https://d2s.semanticscience.org/docs/d2s-services) for the complete documentation.
## Edit this template
You might want to edit or modify this template:
```bash
git clone --recursive https://github.com/MaastrichtU-IDS/d2s-project-template.git
```
## Update submodules
You might want to update the `d2s-core` submodule to get the latest updates for the docker deployments definitions:
```shell
./update_submodules.sh
```
## About
We 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).
The user can transform the input data as RDF using various solutions:
* RML mappings
* 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)
* [BioThings Studio](https://d2s.semanticscience.org/docs/d2s-biothings) (web UI and API)
* DOCKET multiomics provider (Python notebooks and Nextflow)