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'))))