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.

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

Repository Structure

• examples/ - example data and code
• 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 (see also https://github.com/dalito/linkml-project-copier?tab=readme-ov-file#prerequisites):

Poetry

Poetry is a Python project management tool. You will use it in your generated project to manage dependencies and build distribution files. Install Poetry by running:

pipx install poetry
pipx inject poetry "poetry-dynamic-versioning[plugin]"

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 pipx by running:

  pipx install copier
  pipx inject copier jinja2_time

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:

pipx install rust-just

To create a Poetry env with all dependencies you then need to run:

• just setup

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:

poetry 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 example

  poetry run linkml validate tests/data/valid/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 tests/data/valid/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 domain agnostic DCAT-AP extension conform example of an analysis

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

Credits

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