Chem-DCAT-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.

DCAT-AP to LinkML translation

The official DCAT-AP 3.0.0 SHACL shapes where downloaded from the DCAT-AP GitHub repository from the 3.0.0 release folder within the master branch. We chose this shapes definition file, as they are in line with the current DCAT-AP Specification website and because its IRI resolves. It must be noted, that this is not case for the shapes provides in the GitHub 3.0.0 release (respectively the release branch).

The downloaded SHACL shapes were then processed by the dcat_ap_shacl_2_linkml.py to generate two LinkML representations from it:

• dcat_ap_linkml.yaml - an almost 1:1 translation from SHACL to LinkML that could be reused by anyone who wants to.
• dcat_ap_plus.yaml - the LinkML representation of DCAT-AP to which we added the additional constraints, classes and properties we need for our DCAT-AP extension.

Website

https://nfdi-de.github.io/chem-dcat-ap

Repository Structure

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

Developer Documentation

See also the documentation of the template: https://github.com/linkml/linkml-project-copier?tab=readme-ov-file#prerequisites

• uv

  uv is a tool to manage Python projects and for managing isolated Python-based applications. You will use it in your generated project to manage dependencies and build distribution files. Install uv by following their instructions.

  Note: Environments with private pypi repository may need extra configuration (example): export UV_DEFAULT_INDEX=https://nexus.example.com/repository/pypi-all/simple

• Copier

  Copier is a tool for generating projects based on a template (like this one!). It also allows re-configuring the projects and to keep them updated when the original template changes. To insert dates into the template, copier requires jinja2_time in the copier environment. Install both with uv by running:

    uv tool install --with jinja2-time copier

• just

  The project contains a justfile with pre-defined complex commands. To execute these commands you need just as command runner. Install it by running:

  uv tool install rust-just

  To generate project artefacts run:

  • just gen-project: generates all other representations
  • just deploy: deploys site
  • just testdoc: locally builds docs and runs test server

Regenerate schema files from DCAT-AP SHACL shapes

To regenerate the DCAT-AP LinkML representation as well as the PLUS extension run:

uv run python src/dcat_ap_shacl_2_linkml.py

Test data validation and convertion

Validate and test all: just test

Validate a single example dataset using LinkML's validator framework:

• Validate domain agnostic DCAT-AP extension conform AnalysisDataset example

  uv run linkml validate tests/data/valid/AnalysisDataset-001.yaml -s src/chem_dcat_ap/schema/chem_dcat_ap.yaml -C AnalysisDataset
  

• Validate a NMR spectroscopy-specific dataset example conforming to ChemDCAT-AP's SubstanceSampleCharacterizationDataset

  uv run linkml validate tests/data/valid/SubstanceSampleCharacterizationDataset-001.yaml -s src/chem_dcat_ap/schema/chem_dcat_ap.yaml -C SubstanceSampleCharacterizationDataset
  

• Validate a reaction dataset example conforming to ChemDCAT-AP's ReactionMonitoringDataset

  uv run linkml validate tests/data/valid/ReactionMonitoringDataset-001.yaml -s src/chem_dcat_ap/schema/chem_dcat_ap.yaml -C ReactionMonitoringDataset
  

• Validate a chemical reaction example conforming to ChemDCAT-AP's ChemicalReaction

  uv run linkml validate tests/data/valid/ChemicalReaction-001.yaml -s src/chem_dcat_ap/schema/chem_dcat_ap.yaml -C ChemicalReaction
  

• Validate a chemical substance sample example conforming to ChemDCAT-AP's SubstanceSample

  uv run linkml validate tests/data/valid/SubstanceSample-001.yaml -s src/chem_dcat_ap/schema/chem_dcat_ap.yaml -C SubstanceSample
  

• Validate a material sample example conforming to ChemDCAT-AP's MaterialSample

  uv run linkml validate tests/data/valid/MaterialSample-001.yaml -s src/chem_dcat_ap/schema/chem_dcat_ap.yaml -C MaterialSample
  

To convert the test data into a TTL graph run:

• Convert the domain agnostic DCAT-AP+ based example of a AnalysisDataset

  uv run linkml-convert -t ttl tests/data/valid/AnalysisDataset-001.yaml -s src/chem_dcat_ap/schema/chem_dcat_ap.yaml -P "_base=https://search.nfdi4chem.de/dataset/" -C AnalysisDataset
  

• Convert a NMR spectroscopy-specific dataset example conforming to ChemDCAT-AP's SubstanceSampleCharacterizationDataset

  uv run linkml-convert -t ttl tests/data/valid/SubstanceSampleCharacterizationDataset-001.yaml -s src/chem_dcat_ap/schema/chem_dcat_ap.yaml -P "_base=https://search.nfdi4chem.de/dataset/" -C SubstanceSampleCharacterizationDataset
  

• Convert a reaction dataset example conforming to ChemDCAT-AP's ReactionMonitoringDataset

  uv run linkml-convert -t ttl tests/data/valid/ReactionMonitoringDataset-001.yaml -s src/chem_dcat_ap/schema/chem_dcat_ap.yaml -P "_base=https://search.nfdi4chem.de/dataset/" -C ReactionMonitoringDataset
  

• Convert a material sample example conforming to ChemDCAT-AP's MaterialSample

  uv run linkml-convert -t ttl tests/data/valid/MaterialSample-001.yaml -s src/chem_dcat_ap/schema/chem_dcat_ap.yaml -P "_base=https://search.nfdi4chem.de/dataset/" -C MaterialSample
  

• Convert a chemical substance sample example conforming to ChemDCAT-AP's SubstanceSample

  uv run linkml-convert -t ttl tests/data/valid/SubstanceSample-001.yaml -s src/chem_dcat_ap/schema/chem_dcat_ap.yaml -P "_base=https://search.nfdi4chem.de/dataset/" -C SubstanceSample
  

• Convert a chemical reaction example conforming to ChemDCAT-AP's ChemicalReaction

  uv run linkml-convert -t ttl tests/data/valid/ChemicalReaction-001.yaml -s src/chem_dcat_ap/schema/chem_dcat_ap.yaml -P "_base=https://search.nfdi4chem.de/dataset/" -C ChemicalReaction
  

Build GitHub pages docs locally

````commandline
uv run mkdocs serve
````
````commandline
rm -rf docs/elements/*.md && uv run gen-doc  -d docs/elements src/chem_dcat_ap/schema/chem_dcat_ap.yaml
````

Credits

This project was initially created with linkml-project-cookiecutter. and later migrated to linkml-project-copier.