Source code for bioregistry.external.cheminf

# -*- coding: utf-8 -*-

"""Download the Chemical Information Ontology registry (children of ``CHEMINF:000464``).

To convert CHEMINF from OWL to OBO Graph JSON, do the following:

.. code-block:: sh

    $ robot convert --input cheminf.owl --format json --output cheminf.json

See the OBO Foundry workflow for preparing a docker container that has ROBOT available

import json

from bioregistry.constants import EXTERNAL
from bioregistry.utils import get_ols_descendants

__all__ = [

DIRECTORY.mkdir(exist_ok=True, parents=True)
PROCESSED_PATH = DIRECTORY / "processed.json"


[docs]def get_cheminf(force_download: bool = False): """Get the Chemical Information Ontology registry.""" if PROCESSED_PATH.exists() and not force_download: with as file: return json.load(file) rv = get_ols_descendants(ontology="cheminf", uri=BASE_URL, force_download=force_download) with"w") as file: json.dump(rv, file, indent=2, sort_keys=True) return rv
if __name__ == "__main__": print(len(get_cheminf(force_download=True))) # noqa:T201