How to use ontobio - 5 common examples

def make_ontology_from_local_file(file_name: str):
    print("Creating ontology from file: " + file_name)
    return ontobio.ontol_factory.OntologyFactory().create(file_name)

cp = subprocess.run(['owltools', file_name, '-o', '-f', 'json', temp_file_name])
        # robot commented out because it is giving a NullPointerException on umls_semantictypes.owl
#        cp = subprocess.run(['robot', 'convert', '--input', file_name, '--output', temp_file_name])
        if cp.stdout is not None:
            log_message(message="OWL convert result: " + cp.stdout, ontology_name=None, output_stream=sys.stdout)
        if cp.stderr is not None:
            log_message(message="OWL convert result: " + cp.stderr, ontology_name=None, output_stream=sys.stderr)
        assert cp.returncode == 0
        json_file = file_name_without_ext + ".json"
        shutil.move(temp_file_name, json_file)
        size = os.path.getsize(json_file)
        log_message(message="Reading ontology JSON file: " + json_file + "; size: " + "{0:.2f}".format(size/1024) + " KiB",
                    ontology_name=None)
#        if not USE_ONTOBIO_JSON_CACHE:
#            delete_ontobio_cache_json(file_name)
        ont_return = ontobio.ontol_factory.OntologyFactory().create(json_file, ignore_cache=True)
    else:
        size = os.path.getsize(file_name_with_pickle_ext)
        log_message("Reading ontology file: " + file_name_with_pickle_ext + "; size: " + "{0:.2f}".format(size/1024) + " KiB", ontology_name=None)
        ont_return = pickle.load(open(file_name_with_pickle_ext, "rb"))
    return ont_return

# Once robot no longer gives a NullPointerException, we can use it like this:
            #        cp = subprocess.run(['robot', 'convert', '--input', file_name, '--output', temp_file_name])
            if cp.stdout is not None:
                kg2_util.log_message(message="OWL convert result: " + cp.stdout, ontology_name=None, output_stream=sys.stdout)
            if cp.stderr is not None:
                kg2_util.log_message(message="OWL convert result: " + cp.stderr, ontology_name=None, output_stream=sys.stderr)
            assert cp.returncode == 0
            json_file = file_name_without_ext + ".json"
            shutil.move(temp_file_name, json_file)
        else:
            json_file = file_name
        size = os.path.getsize(json_file)
        kg2_util.log_message(message="Reading ontology JSON file: " + json_file + "; size: " + "{0:.2f}".format(size/1024) + " KiB",
                             ontology_name=None)

        ont_return = ontobio.ontol_factory.OntologyFactory().create(json_file, ignore_cache=True)
    else:
        size = os.path.getsize(file_name_with_pickle_ext)
        kg2_util.log_message("Reading ontology file: " + file_name_with_pickle_ext + "; size: " + "{0:.2f}".format(size/1024) + " KiB", ontology_name=None)
        ont_return = pickle.load(open(file_name_with_pickle_ext, "rb"))
    return ont_return

# Once robot no longer gives a NullPointerException, we can use it like this:
            #        cp = subprocess.run(['robot', 'convert', '--input', file_name, '--output', temp_file_name])
            if cp.stdout is not None:
                kg2_util.log_message(message="OWL convert result: " + cp.stdout, ontology_name=None, output_stream=sys.stdout)
            if cp.stderr is not None:
                kg2_util.log_message(message="OWL convert result: " + cp.stderr, ontology_name=None, output_stream=sys.stderr)
            assert cp.returncode == 0
            json_file = file_name_without_ext + ".json"
            shutil.move(temp_file_name, json_file)
        else:
            json_file = file_name
        size = os.path.getsize(json_file)
        kg2_util.log_message(message="Reading ontology JSON file: " + json_file + "; size: " + "{0:.2f}".format(size/1024) + " KiB",
                             ontology_name=None)

        ont_return = ontobio.ontol_factory.OntologyFactory().create(json_file, ignore_cache=True)
    else:
        size = os.path.getsize(file_name_with_pickle_ext)
        kg2_util.log_message("Reading ontology file: " + file_name_with_pickle_ext + "; size: " + "{0:.2f}".format(size/1024) + " KiB", ontology_name=None)
        ont_return = pickle.load(open(file_name_with_pickle_ext, "rb"))
    return ont_return

def get_nodes_dict_from_ontology_dict(ont_dict: dict,
                                      map_curie_to_biolink_category: dict,
                                      category_label_to_iri_mapper: callable):
    ontology = ont_dict['ontology']
    assert type(ontology) == ontobio.ontol.Ontology
    ontology_iri = ont_dict['id']
    assert ontology_iri.startswith('http:')
    ontology_curie_id = shorten_iri_to_curie(ontology_iri)

    ret_dict = {ontology_curie_id: {
        'id':  ontology_curie_id,
        'iri': ontology_iri,
        'full name': ont_dict['title'],
        'name': ont_dict['title'],
        'category': category_label_to_iri_mapper('data source'),
        'category label': 'data source',
        'description': ont_dict['description'],
        'synonyms': None,
        'xrefs': None,
        'creation date': None,
        'update date': ont_dict['file last modified timestamp'],