def test_awe_scope_map():
"""
Text axiom weight estimation, syn scopes
"""
ont = Ontology()
assert ont.nodes() == []
lexmap = LexicalMapEngine()
ont.add_node('X:1', 'x1')
ont.add_node('Y:1', 'y1')
ont.add_node('Z:1', 'z1')
ont.add_synonym(Synonym('X:1', val='related', pred='hasRelatedSynonym'))
ont.add_synonym(Synonym('Y:1', val='related', pred='hasRelatedSynonym'))
ont.add_synonym(Synonym('Y:1', val='exact', pred='hasExactSynonym'))
ont.add_synonym(Synonym('Z:1', val='exact', pred='hasExactSynonym'))
lexmap.index_ontology(ont)
xg = lexmap.get_xref_graph()
df = lexmap.as_dataframe(xg)
print(df.to_csv(sep="\t"))
P_XY = lexmap.weighted_axioms('X:1', 'Y:1', xg)
P_YZ = lexmap.weighted_axioms('Y:1', 'Z:1', xg)
logging.info('P_XY={} P_XZ={}'.format(P_XY, P_YZ))
assert P_XY[2] > P_XY[0]
assert P_XY[2] > P_XY[1]
assert P_XY[2] > P_XY[3]
assert P_XY[2] < P_YZ[2]
def test_awe_match_pairs():
"""
Text axiom weight estimation
"""
ont = Ontology()
assert ont.nodes() == []
lexmap = LexicalMapEngine(
config={
'match_weights': [{
'prefix1': 'X',
'prefix2': 'Y',
'weights': [1.0, -1.0, 2.0, 0.0]
}]
})
ont.add_node('X:1', 'foo 1')
ont.add_node('Y:1', 'foo 1')
lexmap.index_ontology(ont)
xg = lexmap.get_xref_graph()
df = lexmap.as_dataframe(xg)
print(df.to_csv(sep="\t"))
P_XY = lexmap.weighted_axioms('X:1', 'Y:1', xg)
P_YX = lexmap.weighted_axioms('Y:1', 'X:1', xg)
logging.info('P_XY={} P_YX={}'.format(P_XY, P_YX))
assert P_XY[0] > P_XY[1]
assert P_XY[0] == P_YX[1]
def test_awe_1_to_1():
"""
Text axiom weight estimation
"""
ont = Ontology()
assert ont.nodes() == []
lexmap = LexicalMapEngine(
config={
'cardinality_weights': [{
'prefix1': 'X',
'prefix2': 'Y',
'cardinality': '11',
'weights': [-1.0, -1.0, 2.0, 0.0]
}]
})
ont.add_node('X:1', 'foo 1')
ont.add_node('Y:1', 'foo 1')
ont.add_node('Z:1a', 'foo 1')
ont.add_node('Z:1b', 'foo 1')
lexmap.index_ontology(ont)
xg = lexmap.get_xref_graph()
df = lexmap.as_dataframe(xg)
print(df.to_csv(sep="\t"))
P_XY = lexmap.weighted_axioms('X:1', 'Y:1', xg)
P_XZ = lexmap.weighted_axioms('X:1', 'Z:1a', xg)
logging.info('P_XY={} P_XZ={}'.format(P_XY, P_XZ))
assert P_XY[2] > P_XZ[2]
def test_mutable():
"""
Test mutability of ontology class
"""
ont = Ontology()
ont.add_node('TEST:1', 'foo bar')
ont.add_node('TEST:2', 'bar foo')
ont.add_node('TEST:3', 'foo bar')
ont.add_node('TEST:4', 'wiz')
syn = Synonym('TEST:4', val='bar foo', pred='hasExactSynonym')
ont.add_synonym(syn)
w = GraphRenderer.create('obo')
w.write(ont)
for n in ont.nodes():
meta = ont._meta(n)
print('{} -> {}'.format(n, meta))
assert ont.label('TEST:1') == 'foo bar'
assert ont.synonyms('TEST:1') == []
assert ont.synonyms('TEST:4')[0].val == 'bar foo'
def create_gene_terms():
print('Creating gene terms')
handle = os.path.join(FIXTURE_DIR, 'hgnc.json')
with open(handle, 'r', encoding='utf-8') as f:
hgnc_json = f.read()
g = obograph_util.convert_json_object(json.loads(hgnc_json))
ont = Ontology(handle=handle, payload=g)
gene_terms = []
for n_id in ont.nodes():
n_dict = ont.node(n_id)
if 'type' in n_dict:
if ont.node_type(n_id) == 'CLASS':
for t in n_dict['meta']['basicPropertyValues']:
if t['pred'] == 'http://ncicb.nci.nih.gov/xml/owl/EVS/Hugo.owl#Approved_Symbol':
symbol = t['val']
if not symbol.endswith('~withdrawn'):
# print('{} {}'.format(n_id, symbol))
gene_terms.append(
GeneTerm(term_id=n_id, label=symbol))
break
GeneTerm.objects.bulk_create(gene_terms)
def test_awe_xref_weights():
"""
Text axiom weight estimation, when provided with defaults
"""
ont = Ontology()
assert ont.nodes() == []
lexmap = LexicalMapEngine(
config={
'xref_weights': [
{
'left': 'X:1',
'right': 'Y:1',
'weights': [100.0, 0.0, 0.0, 0.0]
},
{
'left': 'Z:1',
'right': 'Y:1',
'weights': [0.0, 100.0, 0.0, 0.0]
},
]
})
ont.add_node('X:1', 'foo')
ont.add_node('Y:1', 'foo')
ont.add_node('Z:1', 'foo')
lexmap.index_ontology(ont)
xg = lexmap.get_xref_graph()
df = lexmap.as_dataframe(xg)
print(df.to_csv(sep="\t"))
P_XY = lexmap.weighted_axioms('X:1', 'Y:1', xg)
P_YZ = lexmap.weighted_axioms('Y:1', 'Z:1', xg)
logging.info('P_XY={} P_XZ={}'.format(P_XY, P_YZ))
assert P_XY[0] > P_XY[1]
assert P_XY[0] > P_XY[2]
assert P_XY[0] > P_XY[3]
assert P_YZ[0] > P_YZ[1]
assert P_YZ[0] > P_YZ[2]
assert P_YZ[0] > P_YZ[3]
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]