def get_statements(self):
for u_data, v_data, k, d in self.graph.edges(keys=True, data=True):
# We only interpret causal relations, not correlations
if d[pc.RELATION] not in pc.CAUSAL_RELATIONS:
self.unhandled.append((u_data, v_data, k, d))
continue
# If the left or right-hand sides involve complex abundances,
# add them as statements
for node_ix, node in enumerate((u_data, v_data)):
if isinstance(node, dsl.ComplexAbundance):
self._get_enum_complex(u_data, v_data, k, d, node_ix)
subj_activity = _get_activity_condition(d.get(pc.SUBJECT))
obj_activity = _get_activity_condition(d.get(pc.OBJECT))
obj_to_loc = _get_translocation_target(d.get(pc.OBJECT))
# If the object is a translocation, this represents a controlled
# translocation, which we currently do not represent
if obj_to_loc:
self.unhandled.append((u_data, v_data, k, d))
logger.info(
"Controlled translocations are currently not "
"handled: %s)", edge_to_bel(u_data, v_data, d))
continue
# Modification, e.g.
# x(Foo) -> p(Bar, pmod(Ph))
# act(x(Foo)) -> p(Bar, pmod(Ph))
if isinstance(v_data, dsl.Protein) and \
has_protein_modification(v_data):
if obj_activity:
logger.info(
"Ignoring object activity modifier in "
"modification statement: %s, %s, %s, %s", u_data,
v_data, k, d)
else:
self._get_modification(u_data, v_data, k, d)
elif obj_activity:
# If the agents on the left and right hand sides are the same,
# then get an active form:
# ActiveForm
# p(Foo, {variants}) ->/-| act(p(Foo))
# Also Composite active forms:
# compositeAbundance(p(Foo, pmod('Ph', 'T')),
# p(Foo, pmod('Ph', 'Y'))) ->/-|
# act(p(Foo))
if not subj_activity and _proteins_match(u_data, v_data):
self._get_active_form(u_data, v_data, k, d)
# Gef
# act(p(Foo)) => gtp(p(Foo))
# Gap
# act(p(Foo)) =| gtp(p(Foo))
elif subj_activity and _rel_is_direct(d) and \
obj_activity.activity_type == 'gtpbound':
self._get_gef_gap(u_data, v_data, k, d)
# Activation/Inhibition
# x(Foo) -> act(x(Foo))
# act(x(Foo)) -> act(x(Foo))
# GtpActivation
# gtp(p(Foo)) => act(p(Foo))
else:
self._get_regulate_activity(u_data, v_data, k, d)
# Activations involving biological processes or pathologies
# x(Foo) -> bp(Bar)
elif isinstance(v_data, (dsl.BiologicalProcess, dsl.Pathology)):
self._get_regulate_activity(u_data, v_data, k, d)
# Regulate amount
# x(Foo) -> p(Bar)
# x(Foo) -> r(Bar)
# act(x(Foo)) -> p(Bar):
# x(Foo) -> deg(p(Bar))
# act(x(Foo)) ->/-| deg(p(Bar))
elif (isinstance(v_data, (
dsl.Protein,
dsl.Rna,
dsl.Abundance,
dsl.MicroRna,
dsl.NamedComplexAbundance,
)) and not obj_activity):
self._get_regulate_amount(u_data, v_data, k, d)
# Controlled conversions
# x(Foo) -> rxn(reactants(r1,...,rn), products(p1,...pn))
# act(x(Foo)) -> rxn(reactants(r1,...,rn), products(p1,...pn))
# Note that we can't really handle statements where the relation
# is decreases, as inhibition of a reaction match the semantics
# of a controlled conversion
elif (isinstance(v_data, dsl.Reaction)
and d[pc.RELATION] in pc.CAUSAL_INCREASE_RELATIONS):
self._get_conversion(u_data, v_data, k, d)
# UNHANDLED
# rxn(reactants(r1,...,rn), products(p1,...pn))
# Complex(a,b)
# p(A, pmod('ph')) -> Complex(A, B)
# Complex(A-Ph, B)
# Complexes
# complex(x(Foo), x(Bar), ...)
else:
self.unhandled.append((u_data, v_data, k, d))
def get_statements(self):
for u_data, v_data, k, d in self.graph.edges(keys=True, data=True):
# We only interpret causal relations, not correlations
if d[pc.RELATION] not in pc.CAUSAL_RELATIONS:
self.unhandled.append((u_data, v_data, k, d))
continue
# If the left or right-hand sides involve complex abundances,
# add them as statements
for node_ix, node_data in enumerate((u_data, v_data)):
if node_data[pc.FUNCTION] == pc.COMPLEX:
self._get_complex(u_data, v_data, k, d, node_ix)
subj_activity = _get_activity_condition(d.get(pc.SUBJECT))
obj_activity = _get_activity_condition(d.get(pc.OBJECT))
obj_to_loc = _get_translocation_target(d.get(pc.OBJECT))
# If the object is a translocation, this represents a controlled
# translocation, which we currently do not represent
if obj_to_loc:
self.unhandled.append((u_data, v_data, k, d))
logger.info("Controlled translocations are currently not "
"handled: %s)", edge_to_bel(u_data, v_data, d))
continue
v_func = v_data[pc.FUNCTION]
# Modification, e.g.
# x(Foo) -> p(Bar, pmod(Ph))
# act(x(Foo)) -> p(Bar, pmod(Ph))
if v_func == pc.PROTEIN and \
has_protein_modification(v_data):
if obj_activity:
logger.info("Ignoring object activity modifier in "
"modification statement: %s, %s, %s, %s",
u_data, v_data, k, d)
else:
self._get_modification(u_data, v_data, k, d)
elif obj_activity:
# If the agents on the left and right hand sides are the same,
# then get an active form:
# ActiveForm
# p(Foo, {variants}) ->/-| act(p(Foo))
# Also Composite active forms:
# compositeAbundance(p(Foo, pmod('Ph', 'T')),
# p(Foo, pmod('Ph', 'Y'))) ->/-|
# act(p(Foo))
if not subj_activity and _proteins_match(u_data, v_data):
self._get_active_form(u_data, v_data, k, d)
# Gef
# act(p(Foo)) => gtp(p(Foo))
# Gap
# act(p(Foo)) =| gtp(p(Foo))
elif subj_activity and _rel_is_direct(d) and \
obj_activity.activity_type == 'gtpbound':
self._get_gef_gap(u_data, v_data, k, d)
# Activation/Inhibition
# x(Foo) -> act(x(Foo))
# act(x(Foo)) -> act(x(Foo))
# GtpActivation
# gtp(p(Foo)) => act(p(Foo))
else:
self._get_regulate_activity(u_data, v_data, k, d)
# Activations involving biological processes or pathologies
# x(Foo) -> bp(Bar)
elif v_func in (pc.BIOPROCESS, pc.PATHOLOGY):
self._get_regulate_activity(u_data, v_data, k, d)
# Regulate amount
# x(Foo) -> p(Bar)
# x(Foo) -> r(Bar)
# act(x(Foo)) -> p(Bar):
# x(Foo) -> deg(p(Bar))
# act(x(Foo)) ->/-| deg(p(Bar))
elif v_data.function in (pc.PROTEIN, pc.RNA, pc.ABUNDANCE,
pc.COMPLEX, pc.MIRNA) and not obj_activity:
self._get_regulate_amount(u_data, v_data, k, d)
# Controlled conversions
# x(Foo) -> rxn(reactants(r1,...,rn), products(p1,...pn))
# act(x(Foo)) -> rxn(reactants(r1,...,rn), products(p1,...pn))
# Note that we can't really handle statements where the relation
# is decreases, as inhibition of a reaction match the semantics
# of a controlled conversion
elif v_data.function == pc.REACTION and \
d[pc.RELATION] in pc.CAUSAL_INCREASE_RELATIONS:
self._get_conversion(u_data, v_data, k, d)
# UNHANDLED
# rxn(reactants(r1,...,rn), products(p1,...pn))
# Complex(a,b)
# p(A, pmod('ph')) -> Complex(A, B)
# Complex(A-Ph, B)
# Complexes
# complex(x(Foo), x(Bar), ...)
else:
self.unhandled.append((u_data, v_data, k, d))
