gaidet-declaration/generate_ontology.py at main · panbibliotekar/gaidet-declaration · GitHub

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# /// script
# requires-python = ">=3.10"
# dependencies = [
#     "bioregistry",
#     "click",
#     "pyobo>=0.12.6",
#     "pyyaml",
# ]
# ///

"""Generate ontology artifacts for GAIDeT."""

from pathlib import Path

import bioregistry
import click
import yaml

from pyobo import Annotation, Reference, Term, build_ontology
from pyobo.struct.typedef import (
    exact_match,
    has_contributor,
    has_ontology_root_term,
    label,
    mapping_has_justification,
)

HERE = Path(__file__).parent.resolve()
TERMS_PATH = HERE.joinpath("_data", "terms.yml")
OWL_PATH = HERE.joinpath("gaidet.owl")

CURIE_PREFIX = "gaidet"
URI_PREFIX = "https://w3id.org/gaidet/"  # TODO need PURL scheme

ONTOLOGY_IRI = "https://w3id.org/gaidet/gaidet.owl"
NAME = "Generative Artificial Intelligence Delegation Taxonomy"
DESCRIPTION = "An extension/complement to Contributor Roles Taxonomy and the Contributor Roles Ontology for generative artificial intelligence."
REPOSITORY = "https://github.com/panbibliotekar/gaidet-declaration"
ROOT = Reference(prefix="cro", identifier="0000000", name="contributor role")


def _annotate_mappings(term: Term, record) -> None:
    for mapping in record.get("mappings", []):
        predicate = Reference.from_curie(mapping["predicate"])
        obj = Reference.from_curie(mapping["object"])
        term.annotate_object(
            predicate,
            obj,
            annotations=[
                Annotation(
                    mapping_has_justification,
                    Reference.from_curie(mapping["mapping_justification"]),
                ),
                Annotation(has_contributor, Reference.from_curie(mapping["contributor"])),
            ],
        )


@click.command()
def main() -> None:
    """Generate ontology artifacts for GAIDeT."""
    bioregistry.add_resource(
        bioregistry.Resource(
            prefix=CURIE_PREFIX,
            uri_format=URI_PREFIX + "$1",
            repository=REPOSITORY,
            description=DESCRIPTION,
        )
    )

    records = yaml.safe_load(TERMS_PATH.read_text())
    terms = [Term(reference=ROOT)]
    for record in records.values():
        term = Term(
            reference=Reference(prefix=CURIE_PREFIX, identifier=record["id"], name=record["label"])
        )
        term.annotate_string(label, record["label_uk"], language="uk")
        term.append_parent(ROOT)
        _annotate_mappings(term, record)
        terms.append(term)

        for child in record["terms"]:
            child_term = Term.from_triple(
                prefix=CURIE_PREFIX, identifier=child["id"], name=child["label"]
            )
            child_term.annotate_string(label, child["label_uk"], language="uk")
            child_term.append_parent(term)
            _annotate_mappings(child_term, child)
            terms.append(child_term)

    ontology = build_ontology(
        prefix=CURIE_PREFIX,
        terms=terms,
        typedefs=[
            exact_match,
            has_ontology_root_term,
            mapping_has_justification,
            label,
            has_contributor,
        ],
        root_terms=[ROOT],
        ontology_iri=ONTOLOGY_IRI,
    )
    ontology.write_owl(OWL_PATH)


if __name__ == "__main__":
    main()