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_translocation(self):
self.assertEqual(
self.add_edge(source_modifier=secretion()),
self.add_edge(source_modifier=secretion()),
)
self.assertEqual(
self.add_edge(source_modifier=secretion()),
self.add_edge(
source_modifier=translocation(INTRACELLULAR, EXTRACELLULAR)),
)
def test_translocation(self):
self.assertEqual(
self.add_edge(subject_modifier=secretion()),
self.add_edge(subject_modifier=secretion()),
)
self.assertEqual(
self.add_edge(subject_modifier=secretion()),
self.add_edge(subject_modifier=translocation(
from_loc=intracellular, to_loc=extracellular)),
)
def test_subject_translocation_custom_to_loc(self, mock):
self.graph.add_increases(
Protein(name='F2', namespace='HGNC'),
Protein(name='EDN1', namespace='HGNC'),
evidence=
'In endothelial cells, ET-1 secretion is detectable under basal conditions, whereas thrombin induces its secretion.',
citation='10473669',
subject_modifier=translocation(
from_loc=Entity(namespace='TEST', name='A'),
to_loc=Entity(namespace='GO', name='extracellular space'),
))
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()
NAMESPACE: BEL_DEFAULT_NAMESPACE,
NAME: 'cat'
}
},
OBJECT: {MODIFIER: DEGRADATION},
}),
(akt1, egfr, {
EVIDENCE: dummy_evidence,
CITATION: citation_1,
RELATION: INCREASES,
SUBJECT: {
MODIFIER: ACTIVITY,
EFFECT: {NAME: 'kin', NAMESPACE: BEL_DEFAULT_NAMESPACE}
},
OBJECT: translocation(
{NAMESPACE: BEL_DEFAULT_NAMESPACE, NAME: 'intracellular'},
{NAMESPACE: BEL_DEFAULT_NAMESPACE, NAME: 'extracellular space'}
),
}),
(Gene('HGNC', 'AKT1', variants=Hgvs('c.308G>A')), tmprss2_erg_gene_fusion, {
EVIDENCE: dummy_evidence,
CITATION: citation_1,
RELATION: CAUSES_NO_CHANGE,
}),
(Gene('HGNC', 'AKT1', variants=Hgvs('c.308G>A')),
Gene('HGNC', 'AKT1', variants=[Hgvs('c.1521_1523delCTT'), Hgvs('c.308G>A'), Hgvs('p.Phe508del')]), {
EVIDENCE: dummy_evidence,
CITATION: citation_1,
RELATION: INCREASES,
SUBJECT: {LOCATION: {NAMESPACE: 'GO', NAME: 'intracellular'}},
}),
(MicroRna('HGNC', 'MIR21'), bcr_jak2_gene_fusion,