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))