def get_observed_stmts(target_agent, observed_agent_forms, fold_change):
stmts = []
for obsf in observed_agent_forms:
obs_agent = Agent(obsf.name, db_refs=obsf.db_refs)
# If the agent has a modification then we make Modification
# statements to check
if obsf.mods:
for mod in obsf.mods:
# Create a Phosphorylation statement corresponding to
# this drug/Ab pair
if fold_change < 1:
stmt = Phosphorylation(target_agent, obs_agent,
mod.residue, mod.position)
else:
stmt = Dephosphorylation(target_agent, obs_agent,
mod.residue, mod.position)
# Otherwise the observed change is in protein amounts so we make
# RegulateAmount statements
else:
if fold_change < 1:
stmt = IncreaseAmount(target_agent, obs_agent)
else:
stmt = DecreaseAmount(target_agent, obs_agent)
stmts.append(stmt)
return stmts
def test_find_contradicts():
st1 = Inhibition(Agent('a'), Agent('b'))
st2 = Activation(Agent('a'), Agent('b'))
st3 = IncreaseAmount(Agent('a'), Agent('b'))
st4 = DecreaseAmount(Agent('a'), Agent('b'))
pa = Preassembler(hierarchies, [st1, st2, st3, st4])
contradicts = pa.find_contradicts()
assert len(contradicts) == 2
for s1, s2 in contradicts:
assert {s1.uuid, s2.uuid} in ({st1.uuid,
st2.uuid}, {st3.uuid, st4.uuid})
def test_find_contradicts():
st1 = Inhibition(Agent('a'), Agent('b'))
st2 = Activation(Agent('a'), Agent('b'))
st3 = IncreaseAmount(Agent('a'), Agent('b'))
st4 = DecreaseAmount(Agent('a'), Agent('b'))
st5 = ActiveForm(
Agent('a', mods=[ModCondition('phosphorylation', None, None, True)]),
'kinase', True)
st6 = ActiveForm(
Agent('a', mods=[ModCondition('phosphorylation', None, None, True)]),
'kinase', False)
pa = Preassembler(hierarchies, [st1, st2, st3, st4, st5, st6])
contradicts = pa.find_contradicts()
assert len(contradicts) == 3
for s1, s2 in contradicts:
assert {s1.uuid,
s2.uuid} in ({st1.uuid,
st2.uuid}, {st3.uuid,
st4.uuid}, {st5.uuid, st6.uuid})
def process_increase_expression_amount(self):
"""Looks for Positive_Regulation events with a specified Cause
and a Gene_Expression theme, and processes them into INDRA statements.
"""
statements = []
pwcs = self.find_event_parent_with_event_child('Positive_regulation',
'Gene_expression')
for pair in pwcs:
pos_reg = pair[0]
expression = pair[1]
cause = self.get_entity_text_for_relation(pos_reg, 'Cause')
target = self.get_entity_text_for_relation(expression, 'Theme')
if cause is not None and target is not None:
theme_node = self.get_related_node(expression, 'Theme')
assert (theme_node is not None)
evidence = self.node_to_evidence(theme_node, is_direct=False)
statements.append(
IncreaseAmount(s2a(cause), s2a(target), evidence=evidence))
return statements
def _get_db_with_pa_stmts():
db = get_temp_db(clear=True)
db_builder = DbBuilder(db)
db_builder.add_text_refs([('12345', 'PMC54321'), ('24680', 'PMC08642'),
('97531', ), ('87687', )])
db_builder.add_text_content([['pubmed-ttl', 'pubmed-abs', 'pmc_oa'],
['pubmed-ttl', 'pubmed-abs', 'manuscripts'],
['pubmed-ttl', 'pubmed-abs', 'pmc_oa'],
['pubmed-ttl', 'pubmed-abs']])
db_builder.add_readings([
# Ref 1
['REACH', 'TRIPS'], # pubmed ttl
['REACH', 'SPARSER'], # pubmed abs
['REACH', 'ISI'], # pmc_oa
# Ref 2
['REACH', 'TRIPS'], # pubmed ttl (new)
['SPARSER'], # pubmed abs
['REACH', 'SPARSER'], # manuscripts
# Ref 3
['SPARSER', 'TRIPS', 'REACH'], # pubmed ttl
['REACH', 'EIDOS', 'SPARSER'], # pubmed abs
['SPARSER'], # pmc oa (new)
# Ref 4
['TRIPS', 'REACH', 'SPARSER'], # pubmed ttl (new)
['REACH', 'SPARSER'], # pubmed abs (new)
])
db_builder.add_raw_reading_statements([
# Ref 1
# pubmed ttl
[Phosphorylation(mek, erk)], # reach
[Phosphorylation(mek, erk, 'T', '124')], # trips
# pubmed abs
[
Phosphorylation(mek, erk),
Inhibition(erk, ras), (Phosphorylation(mek, erk), 'in the body')
], # reach
[
Complex([mek, erk]),
Complex([erk, ras]), (Phosphorylation(None, erk), 'In the body')
], # sparser
# pmc OA
[], # reach
[], # ISI
# Ref 2
# pubmed ttl
[Phosphorylation(map2k1, mapk1)], # reach (new)
[Phosphorylation(map2k1, mapk1, 'T', '124')], # trips (new)
# pubmed abs
[Phosphorylation(map2k1, mapk1)], # sparser
# manuscript
[], # reach
[], # sparser
# Ref 3
# pubmed ttl
[], # sparser
[Inhibition(simvastatin, raf)], # TRIPS
[], # reach
# pubmed abs
[], # reach
[], # eidos
[Activation(map2k1_mg, erk),
Inhibition(simvastatin_ng, raf)], # sparser (new)
# pmc oa
[
Inhibition(simvastatin_ng, raf),
Inhibition(erk, ras),
Activation(ras, raf)
], # sparser (new)
# Ref 4
# pubmed ttl
[], # trips (new)
[], # reach (new)
[], # sparser (new)
# pubmed abstract
[
Activation(kras, braf),
Complex([map2k1, mapk1]),
Complex([kras, braf])
], # reach (new)
[
Complex([kras, braf]),
Complex([mek, erk]),
IncreaseAmount(kras, braf)
], # sparser (new)
])
db_builder.add_databases(['biopax', 'tas', 'bel'])
db_builder.add_raw_database_statements([[
Activation(mek, raf),
Inhibition(erk, ras),
Phosphorylation(mek, erk),
Activation(ras, raf)
], [Inhibition(simvastatin, raf)], [Phosphorylation(mek, erk, 'T',
'124')]])
db_builder.add_pa_statements([(Phosphorylation(mek, erk), [0, 2, 4,
25], [1, 8]),
(Phosphorylation(mek, erk, 'T',
'124'), [1, 28]),
(Phosphorylation(None, erk), [7], [0, 1, 8]),
(Activation(mek, raf), [23]),
(Inhibition(simvastatin, raf), [11, 27]),
(Complex([mek, erk]), [5]),
(Complex([erk, ras]), [6]),
(Inhibition(erk, ras), [3, 24]),
(Phosphorylation(map2k1, mapk1), [10])])
# Add the preassembly update.
pu = db.PreassemblyUpdates(corpus_init=True)
db.session.add(pu)
db.session.commit()
return db