def test_complex_with_complex():
grb2 = Agent('GRB2', db_refs={'HGNC': id('GRB2')})
egfr_grb2 = Agent('EGFR', db_refs={'HGNC': id('EGFR')},
bound_conditions=[BoundCondition(grb2)])
sos1_phos = Agent('SOS1',
mods=[ModCondition('phosphorylation', 'Y', '100')],
db_refs={'HGNC': id('SOS1')})
stmt = Complex([sos1_phos, egfr_grb2])
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert len(belgraph) == 6
assert belgraph.number_of_edges() == 5
egfr_grb2_complex = complex_abundance([egfr_dsl, grb2_dsl])
egfr_grb2_complex_sos1_phos_complex = complex_abundance([
egfr_grb2_complex,
sos1_dsl.with_variants(pmod('Ph', 'Tyr', 100))
])
assert egfr_grb2_complex in belgraph
for member in egfr_grb2_complex.members:
assert member in belgraph
assert egfr_grb2_complex_sos1_phos_complex in belgraph
for member in egfr_grb2_complex_sos1_phos_complex.members:
assert member in belgraph
def test_complex_with_complex():
grb2 = Agent('GRB2', db_refs={'HGNC': id('GRB2')})
egfr_grb2 = Agent('EGFR', db_refs={'HGNC': id('EGFR')},
bound_conditions=[BoundCondition(grb2)])
sos1_phos = Agent('SOS1',
mods=[ModCondition('phosphorylation', 'Y', '100')],
db_refs={'HGNC': id('SOS1')})
stmt = Complex([sos1_phos, egfr_grb2])
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert len(belgraph) == 6
assert belgraph.number_of_edges() == 5
egfr_grb2_complex = complex_abundance([egfr_dsl, grb2_dsl])
egfr_grb2_complex_sos1_phos_complex = complex_abundance([
egfr_grb2_complex,
sos1_dsl.with_variants(pmod('Ph', 'Tyr', 100))
])
assert egfr_grb2_complex in belgraph
for member in egfr_grb2_complex.members:
assert member in belgraph
assert egfr_grb2_complex_sos1_phos_complex in belgraph
for member in egfr_grb2_complex_sos1_phos_complex.members:
assert member in belgraph
def test_regulates_with_multiple_nnotations(self):
"""
3.1.7 http://openbel.org/language/web/version_2.0/bel_specification_version_2.0.html#_regulates_reg
Test nested definitions"""
statement = 'pep(complex(p(HGNC:F3),p(HGNC:F7))) regulates pep(p(HGNC:F9))'
result = self.parser.relation.parseString(statement)
expected_dict = {
SUBJECT: {
MODIFIER: ACTIVITY,
EFFECT: {
NAME: 'pep',
NAMESPACE: BEL_DEFAULT_NAMESPACE
},
TARGET: {
FUNCTION:
COMPLEX,
MEMBERS: [{
FUNCTION: PROTEIN,
NAMESPACE: 'HGNC',
NAME: 'F3'
}, {
FUNCTION: PROTEIN,
NAMESPACE: 'HGNC',
NAME: 'F7'
}]
}
},
RELATION: REGULATES,
OBJECT: {
MODIFIER: ACTIVITY,
EFFECT: {
NAME: 'pep',
NAMESPACE: BEL_DEFAULT_NAMESPACE
},
TARGET: {
FUNCTION: PROTEIN,
NAMESPACE: 'HGNC',
NAME: 'F9'
}
}
}
self.assertEqual(expected_dict, result.asDict())
sub_member_1 = protein('HGNC', 'F3')
self.assert_has_node(sub_member_1)
sub_member_2 = protein('HGNC', 'F7')
self.assert_has_node(sub_member_2)
sub = complex_abundance([sub_member_1, sub_member_2])
self.assert_has_node(sub)
self.assert_has_edge(sub, sub_member_1)
self.assert_has_edge(sub, sub_member_2)
obj = protein('HGNC', 'F9')
self.assert_has_node(obj)
self.assert_has_edge(sub, obj, relation=expected_dict[RELATION])
def flatten_complex_to_bel_node(graph, node):
"""Create complex abundance BEL node.
:param pybel.BELGraph graph: BEL Graph
:param dict node: dictionary of node attributes
:return: BEL node dictionary
:rtype: pybel.dsl.BaseEntity
"""
members = list()
for node_dict in node:
if HGNC in node_dict:
protein_node = protein(namespace=HGNC,
name=node_dict[HGNC_SYMBOL],
identifier=node_dict[HGNC])
members.append(protein_node)
elif UNIPROT in node_dict:
protein_node = protein(namespace=UNIPROT.upper(),
name=node_dict[UNIPROT],
identifier=node_dict[UNIPROT])
members.append(protein_node)
else:
protein_node = protein(namespace=KEGG.upper(),
name=node_dict[KEGG_ID],
identifier=node_dict[KEGG_ID])
members.append(protein_node)
complex_members = complex_abundance(members=members)
graph.add_node_from_data(complex_members)
return complex_members
def test_complex_with_name(self):
"""Test what happens with a named complex.
.. code-block::
complex(SCOMP:"9-1-1 Complex") hasComponent p(HGNC:HUS1)
complex(SCOMP:"9-1-1 Complex") hasComponent p(HGNC:RAD1)
complex(SCOMP:"9-1-1 Complex") hasComponent p(HGNC:RAD9A)
"""
hus1 = protein(namespace='HGNC', name='HUS1')
rad1 = protein(namespace='HGNC', name='RAD1')
rad9a = protein(namespace='HGNC', name='RAD9A')
members = [hus1, rad1, rad9a]
nine_one_one = complex_abundance(members=members,
namespace='SCOMP',
name='9-1-1 Complex')
graph = BELGraph()
graph.add_node_from_data(nine_one_one)
self.assertIn(nine_one_one, graph)
self.assertIn(hus1, graph)
self.assertIn(rad1, graph)
self.assertIn(rad9a, graph)
def test_complex_with_name(self):
"""Tests a what happens with a named complex
.. code-block::
complex(SCOMP:"9-1-1 Complex") hasComponent p(HGNC:HUS1)
complex(SCOMP:"9-1-1 Complex") hasComponent p(HGNC:RAD1)
complex(SCOMP:"9-1-1 Complex") hasComponent p(HGNC:RAD9A)
"""
hus1 = protein(namespace='HGNC', name='HUS1')
rad1 = protein(namespace='HGNC', name='RAD1')
rad9a = protein(namespace='HGNC', name='RAD9A')
members = [hus1, rad1, rad9a]
nine_one_one = complex_abundance(members=members,
namespace='SCOMP',
name='9-1-1 Complex')
node_tuple = (COMPLEX, ) + tuple(member.as_tuple()
for member in members)
self.assertEqual(node_tuple, nine_one_one.as_tuple())
self.assertEqual(hash(node_tuple), hash(nine_one_one))
self.assertEqual(hash_node(node_tuple), nine_one_one.as_sha512())
def test_transphosphorylation():
egfr = Agent('EGFR', db_refs={'HGNC': id('EGFR')})
egfr_dimer = Agent('EGFR',
bound_conditions=[BoundCondition(egfr)],
db_refs={'HGNC': id('EGFR')})
stmt = Transphosphorylation(egfr_dimer, 'Y', '1173')
stmt_hash = stmt.get_hash(refresh=True)
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert belgraph.number_of_nodes() == 3
assert belgraph.number_of_edges() == 3
egfr_dimer_node = complex_abundance([egfr_dsl, egfr_dsl])
egfr_phos_node = egfr_dsl.with_variants(pmod('Ph', 'Tyr', 1173))
edge_data = get_edge_data(belgraph, egfr_dimer_node, egfr_phos_node)
assert edge_data == {
pc.RELATION: pc.DIRECTLY_INCREASES,
pc.ANNOTATIONS: {
'stmt_hash': {
stmt_hash: True
},
'uuid': {
stmt.uuid: True
},
'belief': {
stmt.belief: True
},
},
}, edge_data
def test_transphosphorylation():
egfr = Agent('EGFR', db_refs={'HGNC': id('EGFR')})
egfr_dimer = Agent('EGFR', bound_conditions=[BoundCondition(egfr)],
db_refs={'HGNC': id('EGFR')})
stmt = Transphosphorylation(egfr_dimer, 'Y', '1173')
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert belgraph.number_of_nodes() == 3
assert belgraph.number_of_edges() == 3
egfr_dimer_node = complex_abundance([egfr_dsl, egfr_dsl])
egfr_phos_node = egfr_dsl.with_variants(pmod('Ph', 'Tyr', 1173))
edge_data = get_edge_data(belgraph, egfr_dimer_node, egfr_phos_node)
assert edge_data == {pc.RELATION: pc.DIRECTLY_INCREASES}
def complex_to_bel(complex_dict, nodes, graph: BELGraph):
"""Convert complex abundance to BEL."""
members = list({
nodes[member_id]
for member_id in complex_dict['participants']
if member_id in nodes
})
_, _, _, identifier = parse_id_uri(complex_dict['uri_id'])
complex_bel_node = complex_abundance(members=members, identifier=identifier)
graph.add_node_from_data(complex_bel_node)
return complex_bel_node
def test_complex_with_pmod():
sos1_phos = Agent('SOS1',
mods=[ModCondition('phosphorylation', 'Y', '100')],
db_refs={'HGNC': id('SOS1')})
grb2 = Agent('GRB2', db_refs={'HGNC': id('GRB2')})
egfr = Agent('EGFR', db_refs={'HGNC': id('EGFR')})
stmt = Complex([sos1_phos, grb2, egfr])
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert belgraph.number_of_nodes() == 5
assert belgraph.number_of_edges() == 4
egfr_grb2_sos_phos_tyr_100 = complex_abundance(
[egfr_dsl, grb2_dsl,
sos1_dsl.with_variants(pmod('Ph', 'Tyr', 100))])
assert sos1_dsl in belgraph
assert egfr_grb2_sos_phos_tyr_100 in belgraph
for member in egfr_grb2_sos_phos_tyr_100.members:
assert member in belgraph
def bel_isolated_reconstituted(self, graph: BELGraph):
"""Run the isolated node test."""
self.assertIsNotNone(graph)
self.assertIsInstance(graph, BELGraph)
adgrb1 = protein(namespace='HGNC', name='ADGRB1')
adgrb2 = protein(namespace='HGNC', name='ADGRB2')
adgrb_complex = complex_abundance([adgrb1, adgrb2])
achlorhydria = pathology(namespace='MESHD', name='Achlorhydria')
for node in graph:
self.assertIsInstance(node, BaseEntity)
self.assertIn(adgrb1, graph)
self.assertIn(adgrb2, graph)
self.assertIn(adgrb_complex, graph)
self.assertIn(achlorhydria, graph)
assert_has_edge(self, adgrb_complex, adgrb1, graph)
assert_has_edge(self, adgrb_complex, adgrb2, graph)
def test_complex_with_pmod():
sos1_phos = Agent('SOS1',
mods=[ModCondition('phosphorylation', 'Y', '100')],
db_refs={'HGNC': id('SOS1')})
grb2 = Agent('GRB2', db_refs={'HGNC': id('GRB2')})
egfr = Agent('EGFR', db_refs={'HGNC': id('EGFR')})
stmt = Complex([sos1_phos, grb2, egfr])
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert belgraph.number_of_nodes() == 5
assert belgraph.number_of_edges() == 4
egfr_grb2_sos_phos_tyr_100 = complex_abundance([
egfr_dsl,
grb2_dsl,
sos1_dsl.with_variants(pmod('Ph', 'Tyr', 100))
])
assert sos1_dsl in belgraph
assert egfr_grb2_sos_phos_tyr_100 in belgraph
for member in egfr_grb2_sos_phos_tyr_100.members:
assert member in belgraph
def node_to_bel(node: Dict, graph, hgnc_manager: HgncManager,
chebi_manager: ChebiManager, species) -> BaseEntity:
"""Convert node dictionary to BEL node object."""
node_types = node['entity_type']
identifier, name, namespace = get_valid_node_parameters(
node, hgnc_manager, chebi_manager, species)
members = set()
if namespace == 'hgnc_multiple_entry':
return composite_abundance(process_multiple_proteins(identifier))
elif 'Protein' in node_types:
return protein(namespace=namespace.upper(),
name=name,
identifier=identifier)
elif 'Dna' in node_types:
return gene(namespace=namespace.upper(),
name=name,
identifier=identifier)
elif 'Rna' in node_types:
return rna(namespace=namespace.upper(),
name=name,
identifier=identifier)
elif 'SmallMolecule' in node_types:
return abundance(namespace=namespace.upper(),
name=name,
identifier=identifier)
elif 'PhysicalEntity' in node_types:
return abundance(namespace=namespace.upper(),
name=name,
identifier=identifier)
elif 'Complex' in node_types:
complex_components = node.get('complex_components')
if complex_components:
for component in complex_components:
bel_node = node_to_bel(component, graph, hgnc_manager,
chebi_manager, species)
members.add(bel_node)
if members:
return complex_abundance(name=node.get('display_name'),
members=members,
identifier=identifier,
namespace=namespace.upper())
else:
return NamedComplexAbundance(name=node.get('display_name'),
identifier=identifier,
namespace=namespace.upper())
elif 'Pathway' in node_types:
bioprocess_node = bioprocess(identifier=identifier,
name=name,
namespace=namespace.upper())
graph.add_node_from_data(bioprocess_node)
return bioprocess_node
else:
log.warning('Entity type not recognized', node_types)
)
example_graph = BELGraph()
example_graph.namespace_url['HGNC'] = ''
example_graph.namespace_pattern['DBSNP'] = r'^rs\d+$'
example_graph.annotation_url['Species'] = ''
example_graph.annotation_pattern['Number'] = r'^\d+$'
example_graph.annotation_list['Confidence'] = {'High', 'Low'}
ptk2 = protein(namespace='HGNC', name='PTK2', variants=[pmod('Ph', 'Tyr', 925)])
mapk1 = protein(namespace='HGNC', name='MAPK1')
mapk3 = protein(namespace='HGNC', name='MAPK3')
grb2 = protein(namespace='HGNC', name='GRB2')
sos1 = protein(namespace='HGNC', name='SOS1')
ptk2_rgb2_sos1 = complex_abundance([mapk1, grb2, sos1])
ras_family = protein(namespace='SFAM', name='RAS Family')
pi3k_complex = named_complex_abundance(namespace='SFAM', name='p85/p110 PI3Kinase Complex')
kinase_activity = activity('kin')
catalytic_activity = activity('cat')
gtp_activity = activity('gtp')
c1 = '10446041'
e1 = "FAK also combines with, and may activate, phosphoinositide 3-OH kinase (PI 3-kinase), either directly or " \
"through the Src kinase (13). Finally, there is evidence that Src phosphorylates FAK at Tyr925, creating a" \
" binding site for the complex of the adapter Grb2 and Ras guanosine 5'-triphosphate exchange factor mSOS (10)." \
" These interactions link FAK to signaling pathways that modify the cytoskeleton and activate mitogen-activated" \
" protein kinase (MAPK) cascades (Fig. 3A)."
egfr_dsl = protein(namespace='HGNC', name='EGFR', identifier='3236')
chebi_17534 = abundance(namespace='CHEBI', name='D-glucose',
identifier='17634')
chebi_4170 = abundance(namespace='CHEBI', name='D-glucopyranose 6-phosphate',
identifier='4170')
chebi_17534_to_4170 = reaction(chebi_17534, chebi_4170)
grb2_dsl = protein(namespace='HGNC', name='GRB2', identifier='4566')
sos1_dsl = protein(namespace='HGNC', name='SOS1', identifier='11187')
sos1_phosphorylated_dsl = sos1_dsl.with_variants(pmod('Ph'))
kras_node = protein(namespace='HGNC', name='KRAS', identifier='6407')
egfr_grb2_sos1_complex_dsl = complex_abundance([
egfr_dsl,
grb2_dsl,
sos1_dsl,
])
egfr_grb2_sos1_phos_complex_dsl = complex_abundance([
egfr_dsl,
grb2_dsl,
sos1_phosphorylated_dsl,
])
def draw(g, filename):
ag = nx.nx_agraph.to_agraph(g)
ag.draw(filename, prog='dot')
def test_empty_complex(self):
"""Test that an empty complex causes a failure."""
with self.assertRaises(ValueError):
complex_abundance(members=[])
def complexes_to_bel_node(graph, members):
complex_node = complex_abundance(members=members)
graph.add_node_from_data(complex_node)
return complex_node
def test_complex_abundance(self):
node = complex_abundance(members=[
protein(namespace='HGNC', name='FOS'),
protein(namespace='HGNC', name='JUN')
])
self.assertEqual('complex(p(HGNC:FOS), p(HGNC:JUN))', str(node))
tp53_dsl = protein(namespace='HGNC', name='TP53')
mdm2_dsl = protein(namespace='HGNC', name='MDM2')
egfr_dsl = protein(namespace='HGNC', name='EGFR')
chebi_17534 = abundance(namespace='CHEBI', name='17634')
chebi_4170 = abundance(namespace='CHEBI', name='4170')
chebi_17534_to_4170 = reaction(chebi_17534, chebi_4170)
grb2_dsl = protein(namespace='HGNC', name='GRB2')
sos1_dsl = protein(namespace='HGNC', name='SOS1')
sos1_phosphorylated_dsl = sos1_dsl.with_variants(pmod('Ph'))
kras_node = protein(namespace='HGNC', name='KRAS')
egfr_grb2_sos1_complex_dsl = complex_abundance([
egfr_dsl,
grb2_dsl,
sos1_dsl,
])
egfr_grb2_sos1_phos_complex_dsl = complex_abundance([
egfr_dsl,
grb2_dsl,
sos1_phosphorylated_dsl,
])
def draw(g, filename):
ag = nx.nx_agraph.to_agraph(g)
ag.draw(filename, prog='dot')
