dcat-4C-ap

This is an extension of the DCAT Application Profile v3.0 in LinkML. It is intended to be used by NFDI4Chem & NFDI4Cat as a core that can further be extended in profiles to provide domain specific metadata for a dataset.

Website

https://StroemPhi.github.io/dcat-4C-ap

Repository Structure

• examples/ - example data
• project/ - project files (do not edit these)
• src/ - source files (edit these)
  • dcat_4c_ap
    • schema -- LinkML schema (edit this)
    • datamodel -- generated Python datamodel
• tests/ - Python tests

Developer Documentation

Requirements:

• Poetry must be installed

  • pipx install poetry

• make setup to install Poetry env

• If you want you could run poetry run python src/dcat_ap_shacl_2_linkml.py to recreate the dcat_ap_linkml.yaml from the dcat_ap_shacl.jsonld

• To build the docs locally run:

  • Docs for the autogenerated DCAT-AP LinkML representation

    poetry run gen-doc  -d docs "src/dcat_4C_ap/schema/dcat_ap_linkml.yaml" --template-directory "src/docgen/" && poetry run mkdocs serve
    

  • Docs for the domain agnostic DCAT-AP extension

    poetry run gen-doc  -d docs "src/dcat_4C_ap/schema/dcat_4nfdi_ap.yaml" --template-directory "src/docgen/" && poetry run mkdocs serve
    

  • Docs for the chemistry-specific DCAT-AP extension

    poetry run gen-doc  -d docs "src/dcat_4C_ap/schema/dcat_4c_ap.yaml" --template-directory "src/docgen/" && poetry run mkdocs serve
    

• To validate a test dataset against the model it conforms to run:

  • Validate all example Datasets using the Python test

  make test-python
  

  • Validate all examples using LinkML's run-examples command:

  poetry run linkml-run-examples --output-formats json --output-formats yaml --input-directory src/data/examples --output-directory examples/output --schema src/dcat_4c_ap/schema/dcat_4c_ap.yaml
  

  • Validate a single example dataset using LinkML's validator framework
    • Validate original DCAT-AP conform example

      poetry run linkml validate src/data/examples/Dataset-001.yaml -s src/dcat_4c_ap/schema/dcat_4c_ap.yaml -C Dataset
      

    • Validate domain agnostic DCAT-AP extension conform example

      poetry run linkml validate src/data/examples/AnalysisDataset-001.yaml -s src/dcat_4c_ap/schema/dcat_4c_ap.yaml -C AnalysisDataset
      

    • Validate a NMR spectroscopy-specific DCAT-AP extension conform example

      poetry run linkml validate src/data/examples/NMRAnalysisDataset-001.yaml -s src/dcat_4c_ap/schema/dcat_4c_ap.yaml -C NMRAnalysisDataset
      

• To convert the test datasets of each DCAT-AP profile into a TTL graph run:

  • Convert original DCAT-AP conform example

    poetry run linkml-convert -t ttl src/data/examples/Dataset-001.yaml -s src/dcat_4C_ap/schema/dcat_4c_ap.yaml -P "_base=https://search.nfdi4chem.de/dataset/" -C Dataset
    

  • Convert domain agnostic DCAT-AP extension conform example of an analysis

    poetry run linkml-convert -t ttl src/data/examples/AnalysisDataset-001.yaml -s src/dcat_4C_ap/schema/dcat_4c_ap.yaml -P "_base=https://search.nfdi4chem.de/dataset/" -C AnalysisDataset
    

  • Convert a NMR spectroscopy-specific DCAT-AP extension conform example

    poetry run linkml-convert -t ttl src/data/examples/NMRAnalysisDataset-001.yaml -s src/dcat_4C_ap/schema/dcat_4c_ap.yaml -P "_base=https://search.nfdi4chem.de/dataset/" -C NMRAnalysisDataset
    

• Use the make command to generate project artefacts:

  • make all: make everything
  • make deploy: deploys site

Credits

This project was made with linkml-project-cookiecutter.