def test_p1_active(self):
"""cat(p(HGNC:HSD11B1)) increases deg(a(CHEBI:cortisol))"""
g = BELGraph()
u = protein(name='HSD11B1', namespace='HGNC')
v = abundance(name='cortisol', namespace='CHEBI', identifier='17650')
g.add_increases(
u,
v,
citation={
NAMESPACE: CITATION_TYPE_ONLINE, IDENTIFIER: 'https://www.ncbi.nlm.nih.gov/gene/3290'
},
evidence="Entrez Gene Summary: Human: The protein encoded by this gene is a microsomal enzyme that "
"catalyzes the conversion of the stress hormone cortisol to the inactive metabolite cortisone. "
"In addition, the encoded protein can catalyze the reverse reaction, the conversion of cortisone "
"to cortisol. Too much cortisol can lead to central obesity, and a particular variation in this "
"gene has been associated with obesity and insulin resistance in children. Two transcript "
"variants encoding the same protein have been found for this gene.",
annotations={'Species': '9606'},
source_modifier=activity('cat'),
target_modifier=degradation(),
)
self.assertFalse(is_translocated(g, u))
self.assertFalse(is_degraded(g, u))
self.assertTrue(has_activity(g, u))
self.assertFalse(is_translocated(g, v))
self.assertTrue(is_degraded(g, v))
self.assertFalse(has_activity(g, v))
def test_object_degradation(self):
self.graph.add_increases(
Protein(name='YFG', namespace='HGNC'),
Protein(name='YFG2', namespace='HGNC'),
evidence=n(),
citation=n(),
object_modifier=degradation(),
)
make_dummy_namespaces(self.manager, self.graph)
network = self.manager.insert_graph(self.graph)
self.assertEqual(2, network.nodes.count())
self.assertEqual(1, network.edges.count())
edge = network.edges.first()
def test_convert_degradates(self):
"""Test the conversion of a bel statement like A -> deg(B)."""
microglia = abundance('MeSH', 'Microglia', 'MeSH:D017628')
abeta = abundance('CHEBI', 'amyloid-β', 'CHEBI:64645')
# a(MESH:Microglia) reg deg(a(CHEBI:"amyloid-beta"))
bel_graph = BELGraph()
bel_graph.add_increases(microglia,
abeta,
evidence='10.1038/s41586-018-0368-8',
citation='PubMed:30046111',
object_modifier=degradation())
expected_reified_graph = self.help_make_simple_expected_graph(
microglia, abeta, DEGRADATES, 0, self.help_causal_increases)
reified_graph = reify_bel_graph(bel_graph)
self.help_test_graphs_equal(expected_reified_graph, reified_graph)
def test_subject_degradation_location(self):
self.assertEqual(self.add_edge(source_modifier=degradation()),
self.add_edge(source_modifier=degradation()))
self.assertEqual(
self.add_edge(source_modifier=degradation(
location=Entity(name='somewhere', namespace='GO'))),
self.add_edge(source_modifier=degradation(
location=Entity(name='somewhere', namespace='GO'))))
self.assertNotEqual(
self.add_edge(source_modifier=degradation()),
self.add_edge(source_modifier=degradation(
location=Entity(name='somewhere', namespace='GO'))))