def test_convert_increases_abundance_then_phosphorylates(self):
"""Test the conversion of a bel graph containing one increases abundance and one phosphorylates relationship."""
bel_graph = BELGraph()
bel_graph.add_increases(
oxaliplatin,
reactive_o_species,
evidence='10.1093/jnci/djv394',
citation='26719345',
)
bel_graph.add_directly_increases(
reactive_o_species,
p_tau,
evidence=n(),
citation=n(),
)
re1, re2 = 1, 0
expected_reified_graph = self.help_make_simple_expected_graph(
oxaliplatin, reactive_o_species, INCREASES_ABUNDANCE, re1,
self.help_causal_increases)
expected_reified_graph.add_node(re2,
label=PHOSPHORYLATES,
causal=self.help_causal_increases)
expected_reified_graph.add_edge(reactive_o_species,
re2,
label=REIF_SUBJECT)
expected_reified_graph.add_edge(p_tau, re2, label=REIF_OBJECT)
reified_graph = reify_bel_graph(bel_graph)
self.help_test_graphs_equal(expected_reified_graph, reified_graph)
def test_convert_activates(self):
"""Test the conversion of a bel statement like p(x) -> act(p(y))."""
bel_graph = BELGraph()
bel_graph.add_directly_activates(
cdk5,
casp8,
evidence=n(),
citation=n(),
)
expected_reified_graph = self.help_make_simple_expected_graph(
cdk5, casp8, ACTIVATES, 0, self.help_causal_increases)
reified_graph = reify_bel_graph(bel_graph)
self.help_test_graphs_equal(expected_reified_graph, reified_graph)
def test_convert_phosphorylates(self):
"""Test the conversion of a BEL statement like ``act(p(X)) -> p(Y, pmod(Ph))."""
bel_graph = BELGraph()
bel_graph.add_directly_increases(
cdk5,
p_tau,
evidence=n(),
citation=n(),
subject_modifier=activity('kin'),
)
r_edge = 0
expected_reified_graph = self.help_make_simple_expected_graph(
cdk5, p_tau, PHOSPHORYLATES, r_edge, self.help_causal_increases)
reified_graph = reify_bel_graph(bel_graph)
self.help_test_graphs_equal(expected_reified_graph, reified_graph)
def test_convert_fragments(self):
"""Test the conversion of a bel statement like A -> p(B, frag(?))."""
casp3 = abundance('HGNC', 'CASP3', 'MeSH:D017628')
tau = protein('HGNC', 'MAPT', 'HGNC:6893', variants=fragment())
# act(p(HGNC:CASP3), ma(pep)) increases p(HGNC:MAPT, frag("?"))
bel_graph = BELGraph()
bel_graph.add_increases(casp3,
tau,
evidence='10.1038/s41586-018-0368-8',
citation='PubMed:30046111')
expected_reified_graph = self.help_make_simple_expected_graph(
casp3, tau, FRAGMENTS, 0, self.help_causal_increases)
reified_graph = reify_bel_graph(bel_graph)
self.help_test_graphs_equal(expected_reified_graph, reified_graph)
def generate_bel_network(bel_graph_path: str,
dge_list: List[Gene],
max_adj_p: float,
max_log2_fold_change: float,
min_log2_fold_change: float,
current_disease_ids_path: Optional[str] = None,
disease_associations_path: Optional[str] = None,
collapse: str = None):
"""Generate the protein-protein interaction network.
:param bel_graph_path:
:param dge_list:
:param max_adj_p:
:param max_log2_fold_change:
:param min_log2_fold_change:
:param current_disease_ids_path:
:param disease_associations_path:
:param collapse:
:return: Interaction network with information on differential expression.
"""
# Load and reify the graph
bel_graph = bel_graph_loader(bel_graph_path)
reified = reify_bel_graph(bel_graph, collapse=collapse)
if disease_associations_path is not None:
if current_disease_ids_path:
current_disease_ids = parse_disease_ids(current_disease_ids_path)
else:
current_disease_ids = set()
disease_associations = parse_disease_associations(
disease_associations_path, current_disease_ids)
else:
disease_associations = None
# Build an undirected weighted graph with the remaining interactions based on Entrez gene IDs
network = NetworkNx(
reified,
max_adj_p=max_adj_p,
max_l2fc=max_log2_fold_change,
min_l2fc=min_log2_fold_change,
)
network.set_up_network(dge_list, disease_associations=disease_associations)
return network
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_convert_promote_translation(self):
"""Test the conversion of a bel statement like A -> r(B)"""
# example from Colorectal Cancer Model v2.0.6 @ scai
# act(p(HGNC:CTNNB1), ma(tscript)) increases r(HGNC:BIRC5)
ctnnb1 = protein('HGNC', name='CTNNB1')
birc5 = rna('HGNC', name='BIRC5')
# a(MESH:Microglia) reg deg(a(CHEBI:"amyloid-beta"))
bel_graph = BELGraph()
bel_graph.add_increases(ctnnb1,
birc5,
evidence='10.1038/s41586-018-0368-8',
citation='18075512',
subject_modifier=activity('tscript'))
expected_reified_graph = self.help_make_simple_expected_graph(
ctnnb1, birc5, PROMOTES_TRANSLATION, 0, self.help_causal_increases)
reified_graph = reify_bel_graph(bel_graph)
self.help_test_graphs_equal(expected_reified_graph, reified_graph)
def test_convert_increases_abundance(self):
"""Test the conversion of a bel statement like A -> B, when A and B don't fall in any special case (activity, pmod, ...)."""
bel_graph = BELGraph()
bel_graph.add_increases(
oxaliplatin,
reactive_o_species,
evidence='10.1093/jnci/djv394',
citation='PubMed:26719345',
)
expected_reified_graph = self.help_make_simple_expected_graph(
oxaliplatin,
reactive_o_species,
INCREASES_ABUNDANCE,
0,
self.help_causal_increases,
)
reified_graph = reify_bel_graph(bel_graph)
self.help_test_graphs_equal(expected_reified_graph, reified_graph)
def test_convert_two_phosphorylates(self):
"""Test that two phosphorylations of the same object get different reified nodes."""
bel_graph = BELGraph()
for kinase in (cdk5, gsk3b):
bel_graph.add_directly_increases(
kinase,
p_tau,
evidence=n(),
citation=n(),
subject_modifier=activity('kin'),
)
re1, re2 = 0, 1
expected_reified_graph = self.help_make_simple_expected_graph(
cdk5, p_tau, PHOSPHORYLATES, re1, self.help_causal_increases)
expected_reified_graph.add_node(re2,
label='phosphorylates',
causal=self.help_causal_increases)
expected_reified_graph.add_edge(gsk3b, re2, label=REIF_SUBJECT)
expected_reified_graph.add_edge(p_tau, re2, label=REIF_OBJECT)
reified_graph = reify_bel_graph(bel_graph)
self.help_test_graphs_equal(expected_reified_graph, reified_graph)