def test_subject_has_secretion(self):
"""sec(p(MGI:S100b)) increases a(CHEBI:"nitric oxide")"""
g = BELGraph()
u_node = protein(name='S100b', namespace='MGI')
v_node = abundance(name='nitric oxide', namespace='CHEBI')
u = g.add_node_from_data(u_node)
v = g.add_node_from_data(v_node)
g.add_increases(
u_node,
v_node,
citation='11180510',
evidence=
'S100B protein is also secreted by astrocytes and acts on these cells to stimulate nitric oxide '
'secretion in an autocrine manner.',
annotations={
'Species': '10090',
'Cell': 'astrocyte'
},
subject_modifier=secretion())
self.assertTrue(is_translocated(g, u))
self.assertFalse(is_degraded(g, u))
self.assertFalse(has_activity(g, u))
self.assertFalse(has_causal_in_edges(g, u))
self.assertTrue(has_causal_out_edges(g, u))
self.assertFalse(is_translocated(g, v))
self.assertFalse(is_degraded(g, v))
self.assertFalse(has_activity(g, v))
self.assertTrue(has_causal_in_edges(g, v))
self.assertFalse(has_causal_out_edges(g, v))
def test_object_has_translocation(self):
"""p(HGNC: EGF) increases tloc(p(HGNC: VCP), GOCCID: 0005634, GOCCID: 0005737)"""
g = BELGraph()
u_node = protein(name='EFG', namespace='HGNC')
v_node = protein(name='VCP', namespace='HGNC')
u = g.add_node_from_data(u_node)
v = g.add_node_from_data(v_node)
g.add_qualified_edge(
u_node,
v_node,
relation=INCREASES,
citation='10855792',
evidence=
"Although found predominantly in the cytoplasm and, less abundantly, in the nucleus, VCP can be "
"translocated from the nucleus after stimulation with epidermal growth factor.",
annotations={'Species': '9606'},
object_modifier=translocation(from_loc=entity(
namespace='GO', identifier='0005634'),
to_loc=entity(namespace='GO',
identifier='0005737')))
self.assertFalse(is_translocated(g, u))
self.assertFalse(is_degraded(g, u))
self.assertFalse(has_activity(g, u))
self.assertFalse(has_causal_in_edges(g, u))
self.assertTrue(has_causal_out_edges(g, u))
self.assertTrue(is_translocated(g, v))
self.assertFalse(is_degraded(g, v))
self.assertFalse(has_activity(g, v))
self.assertTrue(has_causal_in_edges(g, v))
self.assertFalse(has_causal_out_edges(g, v))
def test_object_has_secretion(self):
"""p(MGI:Il4) increases sec(p(MGI:Cxcl1))"""
g = BELGraph()
u_node = protein(name='Il4', namespace='MGI')
v_node = protein(name='Cxcl1', namespace='MGI')
u = g.add_node_from_data(u_node)
v = g.add_node_from_data(v_node)
g.add_increases(
u_node,
v_node,
citation='10072486',
evidence=
'Compared with controls treated with culture medium alone, IL-4 and IL-5 induced significantly '
'higher levels of MIP-2 and KC production; IL-4 also increased the production of MCP-1 '
'(Fig. 2, A and B)....we only tested the effects of IL-3, IL-4, IL-5, and IL-13 on chemokine '
'expression and cellular infiltration....Recombinant cytokines were used, ... to treat naive '
'BALB/c mice.',
annotations={
'Species': '10090',
'MeSH': 'bronchoalveolar lavage fluid'
},
object_modifier=secretion())
self.assertFalse(is_translocated(g, u))
self.assertFalse(is_degraded(g, u))
self.assertFalse(has_activity(g, u))
self.assertFalse(has_causal_in_edges(g, u))
self.assertTrue(has_causal_out_edges(g, u))
self.assertTrue(is_translocated(g, v))
self.assertFalse(is_degraded(g, v))
self.assertFalse(has_activity(g, v))
self.assertTrue(has_causal_in_edges(g, v))
self.assertFalse(has_causal_out_edges(g, v))
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))
