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CWL workflows to build the NCATS Translator Red KG, complying with the BioLink model.

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MaastrichtU-IDS/d2s-transform-biolink

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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 tool.

See d2s.semanticscience.org for detailed documentation to run CWL workflows to transform structured data to a target RDF knowledge graph and deploy services.

Requirements

  • pip install the d2s client and cwlref-runner (run workflows of Docker containers) withon Python 3.6+

    sudo apt install d2s cwlref-runner

Create a project

Follow the prompt instructions to create a project in the provided folder:

d2s init project-folder-name

See the d2s.semanticscience.org for the complete documentation.

Edit this template

You might want to edit or modify this template:

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:

./update_submodules.sh

About

We use the Common Workflow Language to describe workflows to transform heterogeneous structured data (CSV, TSV, RDB, XML, JSON) to a target RDF data model (BioLink in those examples).

The user can transform the input data as RDF using various solutions:

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CWL workflows to build the NCATS Translator Red KG, complying with the BioLink model.

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