def get_ontology(self, data_type: DataType, provider=None):
"""Get Ontology"""
ontology = Ontology()
terms_pairs = []
if data_type == DataType.GO:
terms_pairs = Neo4jHelper.run_single_parameter_query(
self.get_ontology_pairs_query.format("GO", "GO"),
None)
elif data_type == DataType.DO:
terms_pairs = Neo4jHelper.run_single_parameter_query(
self.get_ontology_pairs_query.format("DO", "DO"),
None)
elif data_type == DataType.EXPR:
if provider in EXPRESSION_PRVD_SUBTYPE_MAP:
terms_pairs = Neo4jHelper.run_single_parameter_query(
self.get_ontology_pairs_query.format(EXPRESSION_PRVD_SUBTYPE_MAP[provider],
EXPRESSION_PRVD_SUBTYPE_MAP[provider]),
None)
for terms_pair in terms_pairs:
self.add_neo_term_to_ontobio_ontology_if_not_exists(
terms_pair["term1.primaryKey"], terms_pair["term1.name"], terms_pair["term1.type"],
terms_pair["term1.isObsolete"], ontology)
self.add_neo_term_to_ontobio_ontology_if_not_exists(
terms_pair["term2.primaryKey"], terms_pair["term2.name"], terms_pair["term2.type"],
terms_pair["term2.isObsolete"], ontology)
ontology.add_parent(terms_pair["term1.primaryKey"], terms_pair["term2.primaryKey"],
relation="subClassOf" if terms_pair["rel_type"] == "IS_A" else "BFO:0000050")
if data_type == DataType.EXPR and provider == "MGI":
self.add_neo_term_to_ontobio_ontology_if_not_exists("EMAPA_ARTIFICIAL_NODE:99999",
"embryo",
"anatomical_structure",
False,
ontology)
ontology.add_parent("EMAPA_ARTIFICIAL_NODE:99999", "EMAPA:0", relation="subClassOf")
self.add_neo_term_to_ontobio_ontology_if_not_exists("EMAPA_ARTIFICIAL_NODE:99998",
"head",
"anatomical_structure",
False,
ontology)
ontology.add_parent("EMAPA_ARTIFICIAL_NODE:99998", "EMAPA:0", relation="subClassOf")
GeneDescriptionsETL.add_neo_term_to_ontobio_ontology_if_not_exists(
"EMAPA_ARTIFICIAL_NODE:99997",
"gland",
"anatomical_structure",
False,
ontology)
ontology.add_parent("EMAPA_ARTIFICIAL_NODE:99997", "EMAPA:0", relation="subClassOf")
elif data_type == DataType.EXPR and provider == "FB":
GeneDescriptionsETL.add_neo_term_to_ontobio_ontology_if_not_exists(
"FBbt_ARTIFICIAL_NODE:99999",
"organism",
"",
False,
ontology)
ontology.add_parent("FBbt_ARTIFICIAL_NODE:99999",
"FBbt:10000000",
relation="subClassOf")
return ontology
def test_awe_1_to_many_hier():
"""
Text axiom weight estimation
"""
ont = Ontology()
assert ont.nodes() == []
lexmap = LexicalMapEngine()
ont.add_node('X:1', 'foo 1')
ont.add_node('Z:1a', 'foo 1')
ont.add_node('Z:1b', 'foo 1')
ont.add_parent('Z:1b', 'Z:1a')
lexmap.index_ontology(ont)
xg = lexmap.get_xref_graph()
df = lexmap.as_dataframe(xg)
print(df.to_csv(sep="\t"))
P_a = lexmap.weighted_axioms('X:1', 'Z:1a', xg)
P_b = lexmap.weighted_axioms('X:1', 'Z:1b', xg)
logging.info('P_a={} P_b={}'.format(P_a, P_b))
assert P_a[0] > P_a[1]
assert P_b[0] < P_b[1]
assert P_a[0] > P_b[0]
