def test_phosphorylation():
tp = trips.process_text('BRAF phosphorylates MEK1 at Ser222.')
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(isinstance(st, ist.Phosphorylation))
assert(st.residue == 'S')
assert(st.position == '222')
def test_phosphorylation_noresidue():
tp = trips.process_text('BRAF phosphorylates MEK1.')
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(isinstance(st, ist.Phosphorylation))
assert(st.residue is None)
assert(st.position is None)
def test_actmod():
tp = trips.process_text('MEK1 phosphorylated at Ser222 is activated.')
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(isinstance(st, ist.ActiveForm))
assert(isinstance(st.agent.mods[0], ist.ModCondition))
assert(st.agent.mods[0].mod_type == 'phosphorylation')
assert(st.agent.mods[0].residue == 'S')
assert(st.agent.mods[0].position == '222')
def test_actmods():
tp = trips.process_text('BRAF phosphorylated at Ser536 binds MEK1.')
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(isinstance(st, ist.Complex))
braf = st.members[0]
assert(braf.mods[0].mod_type == 'phosphorylation')
assert(braf.mods[0].residue == 'S')
assert(braf.mods[0].position == '536')
def test_ubiquitination():
tp = trips.process_text('MDM2 ubiquitinates TP53.')
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (isinstance(st, ist.Ubiquitination))
assert unicode_strs((tp, st))
assert_grounding_value_or_none(st)
assert_if_hgnc_then_up(st)
assert (st.evidence)
def test_ubiquitination():
tp = trips.process_text('MDM2 ubiquitinates TP53.')
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(isinstance(st, ist.Ubiquitination))
assert unicode_strs((tp, st))
assert_grounding_value_or_none(st)
assert_if_hgnc_then_up(st)
assert(st.evidence)
def test_phosphorylation_nosite():
tp = trips.process_text('BRAF phosphorylates MEK1 at Serine.')
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (isinstance(st, ist.Phosphorylation))
assert (st.residue == 'S')
assert (st.position is None)
assert unicode_strs((tp, st))
assert_if_hgnc_then_up(st)
assert_grounding_value_or_none(st)
assert (st.evidence)
def test_degradation():
tp = trips.process_text('MDM2 degrades TP53.')
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (isinstance(st, ist.DecreaseAmount))
assert (st.subj is not None)
assert (st.obj is not None)
assert unicode_strs((tp, st))
assert_if_hgnc_then_up(st)
assert_grounding_value_or_none(st)
assert (st.evidence)
def test_synthesis():
tp = trips.process_text('NFKB transcribes IKB.')
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (isinstance(st, ist.IncreaseAmount))
assert (st.subj is not None)
assert (st.obj is not None)
assert unicode_strs((tp, st))
assert_if_hgnc_then_up(st)
assert_grounding_value_or_none(st)
assert (st.evidence)
def test_phosphorylation_nosite():
tp = trips.process_text('BRAF phosphorylates MEK1 at Serine.')
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(isinstance(st, ist.Phosphorylation))
assert(st.residue == 'S')
assert(st.position is None)
assert unicode_strs((tp, st))
assert_if_hgnc_then_up(st)
assert_grounding_value_or_none(st)
assert(st.evidence)
def test_bind():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'The receptor tyrosine kinase EGFR binds the growth factor ligand EGF.'
tp = trips.process_text(txt, fname, False)
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (is_complex(st))
assert (len(st.members) == 2)
assert (has_hgnc_ref(st.members[0]))
assert (has_hgnc_ref(st.members[1]))
os.remove(fname)
def test_degradation():
tp = trips.process_text('MDM2 degrades TP53.')
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(isinstance(st, ist.DecreaseAmount))
assert(st.subj is not None)
assert(st.obj is not None)
assert unicode_strs((tp, st))
assert_if_hgnc_then_up(st)
assert_grounding_value_or_none(st)
assert(st.evidence)
def test_synthesis():
tp = trips.process_text('NFKB transcribes IKB.')
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(isinstance(st, ist.IncreaseAmount))
assert(st.subj is not None)
assert(st.obj is not None)
assert unicode_strs((tp, st))
assert_if_hgnc_then_up(st)
assert_grounding_value_or_none(st)
assert(st.evidence)
def test_bind():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'The receptor tyrosine kinase EGFR binds the growth factor ligand EGF.'
tp = trips.process_text(txt, fname, False)
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(is_complex(st))
assert(len(st.members) == 2)
assert(has_hgnc_ref(st.members[0]))
assert(has_hgnc_ref(st.members[1]))
os.remove(fname)
def test_actform_bound():
tp = trips.process_text('HRAS bound to GTP is activated.')
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (isinstance(st, ist.ActiveForm))
assert (isinstance(st.agent.bound_conditions[0], ist.BoundCondition))
assert (st.agent.bound_conditions[0].agent.name == 'GTP')
assert (st.agent.bound_conditions[0].is_bound == True)
assert unicode_strs((tp, st))
assert_if_hgnc_then_up(st)
assert_grounding_value_or_none(st)
assert (st.evidence)
def test_not_bound_to3():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'SOS1 bound to GRB2 binds NRAS that is not bound to BRAF and GTP.'
tp = trips.process_text(txt, fname, False)
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (is_complex(st))
assert (st.members[0].name == 'SOS1')
assert (st.members[1].name == 'NRAS')
assert (len(st.members[0].bound_conditions) == 1)
assert (len(st.members[1].bound_conditions) == 2)
os.remove(fname)
def test_actform_bound():
tp = trips.process_text('HRAS bound to GTP is activated.')
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(isinstance(st, ist.ActiveForm))
assert(isinstance(st.agent.bound_conditions[0], ist.BoundCondition))
assert(st.agent.bound_conditions[0].agent.name == 'GTP')
assert(st.agent.bound_conditions[0].is_bound == True)
assert unicode_strs((tp, st))
assert_if_hgnc_then_up(st)
assert_grounding_value_or_none(st)
assert(st.evidence)
def test_not_bound_to3():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'SOS1 bound to GRB2 binds NRAS that is not bound to BRAF and GTP.'
tp = trips.process_text(txt, fname, False)
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(is_complex(st))
assert(st.members[0].name == 'SOS1')
assert(st.members[1].name == 'NRAS')
assert(len(st.members[0].bound_conditions) == 1)
assert(len(st.members[1].bound_conditions) == 2)
os.remove(fname)
def test_complex_bind3():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'RAF binds to the RAS-GTP complex.'
tp = trips.process_text(txt, fname, False)
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(is_complex(st))
assert(len(st.members) == 2)
assert(st.members[0].name == 'RAF')
assert(st.members[1].name == 'RAS')
assert(len(st.members[1].bound_conditions) == 1)
assert(st.members[1].bound_conditions[0].agent.name == 'GTP')
os.remove(fname)
def test_actmod():
tp = trips.process_text('MEK1 phosphorylated at Ser222 is activated.')
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(isinstance(st, ist.ActiveForm))
assert(isinstance(st.agent.mods[0], ist.ModCondition))
assert(st.agent.mods[0].mod_type == 'phosphorylation')
assert(st.agent.mods[0].residue == 'S')
assert(st.agent.mods[0].position == '222')
assert unicode_strs((tp, st))
assert_if_hgnc_then_up(st)
assert_grounding_value_or_none(st)
assert(st.evidence)
def test_actmods2():
tp = trips.process_text('BRAF phosphorylated at Ser536 binds MEK1.')
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(isinstance(st, ist.Complex))
braf = st.members[0]
assert(braf.mods[0].mod_type == 'phosphorylation')
assert(braf.mods[0].residue == 'S')
assert(braf.mods[0].position == '536')
assert unicode_strs((tp, st, braf))
assert_if_hgnc_then_up(st)
assert_grounding_value_or_none(st)
assert(st.evidence)
def test_actform_muts():
tp = trips.process_text('BRAF V600E is activated.')
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (isinstance(st, ist.ActiveForm))
assert (isinstance(st.agent.mutations[0], ist.MutCondition))
assert (st.agent.mutations[0].residue_from == 'V')
assert (st.agent.mutations[0].residue_to == 'E')
assert (st.agent.mutations[0].position == '600')
assert unicode_strs((tp, st))
assert_if_hgnc_then_up(st)
assert_grounding_value_or_none(st)
assert (st.evidence)
def test_actmods2():
tp = trips.process_text('BRAF phosphorylated at Ser536 binds MEK1.')
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (isinstance(st, ist.Complex))
braf = st.members[0]
assert (braf.mods[0].mod_type == 'phosphorylation')
assert (braf.mods[0].residue == 'S')
assert (braf.mods[0].position == '536')
assert unicode_strs((tp, st, braf))
assert_if_hgnc_then_up(st)
assert_grounding_value_or_none(st)
assert (st.evidence)
def test_complex_bind2():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'The EGFR-EGFR complex binds GRB2.'
tp = trips.process_text(txt, fname, False)
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(is_complex(st))
assert(len(st.members) == 2)
assert(st.members[0].name == 'EGFR')
assert(st.members[1].name == 'GRB2')
assert(len(st.members[0].bound_conditions) == 1)
assert(st.members[0].bound_conditions[0].agent.name == 'EGFR')
os.remove(fname)
def test_not_bound_to4():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'BRAF that is not bound to NRAS and Vemurafenib binds BRAF ' +\
'that is not bound to Vemurafenib.'
tp = trips.process_text(txt, fname, False)
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (is_complex(st))
assert (st.members[0].name == 'BRAF')
assert (st.members[1].name == 'BRAF')
assert (len(st.members[0].bound_conditions) == 2)
assert (len(st.members[1].bound_conditions) == 1)
os.remove(fname)
def trips_process_text():
"""Process text with TRIPS and return INDRA Statements."""
response = request.body.read().decode('utf-8')
body = json.loads(response)
text = body.get('text')
tp = trips.process_text(text)
if tp and tp.statements:
stmts = stmts_to_json(tp.statements)
res = {'statements': stmts}
return res
else:
res = {'statements': []}
return res
def test_not_bound_to4():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'BRAF that is not bound to NRAS and Vemurafenib binds BRAF ' +\
'that is not bound to Vemurafenib.'
tp = trips.process_text(txt, fname, False)
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(is_complex(st))
assert(st.members[0].name == 'BRAF')
assert(st.members[1].name == 'BRAF')
assert(len(st.members[0].bound_conditions) == 2)
assert(len(st.members[1].bound_conditions) == 1)
os.remove(fname)
def test_complex_bind3():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'RAF binds to the RAS-GTP complex.'
tp = trips.process_text(txt, fname, False)
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (is_complex(st))
assert (len(st.members) == 2)
assert (st.members[0].name == 'RAF')
assert (st.members[1].name == 'RAS')
assert (len(st.members[1].bound_conditions) == 1)
assert (st.members[1].bound_conditions[0].agent.name == 'GTP')
os.remove(fname)
def test_bound_phosphorylate():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'RAF, bound to RAF, phosphorylates MEK1.'
tp = trips.process_text(txt, fname, False)
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(is_phosphorylation(st))
assert(st.enz is not None)
assert(st.enz.name == 'RAF')
assert(st.sub is not None)
assert(st.sub.name == 'MAP2K1')
assert(st.residue == None)
os.remove(fname)
def test_actmod():
tp = trips.process_text('MEK1 phosphorylated at Ser222 is activated.')
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (isinstance(st, ist.ActiveForm))
assert (isinstance(st.agent.mods[0], ist.ModCondition))
assert (st.agent.mods[0].mod_type == 'phosphorylation')
assert (st.agent.mods[0].residue == 'S')
assert (st.agent.mods[0].position == '222')
assert unicode_strs((tp, st))
assert_if_hgnc_then_up(st)
assert_grounding_value_or_none(st)
assert (st.evidence)
def test_bound_phosphorylate():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'RAF, bound to RAF, phosphorylates MEK1.'
tp = trips.process_text(txt, fname, False)
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (is_phosphorylation(st))
assert (st.enz is not None)
assert (st.enz.name == 'RAF')
assert (st.sub is not None)
assert (st.sub.name == 'MAP2K1')
assert (st.residue == None)
os.remove(fname)
def test_complex_bind():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'The EGFR-EGF complex binds another EGFR-EGF complex.'
tp = trips.process_text(txt, fname, False)
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (is_complex(st))
assert (len(st.members) == 2)
assert (has_hgnc_ref(st.members[0]))
assert (has_hgnc_ref(st.members[1]))
assert (st.members[0].bound_conditions)
assert (st.members[1].bound_conditions)
os.remove(fname)
def test_actform_muts():
tp = trips.process_text('BRAF V600E is activated.')
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(isinstance(st, ist.ActiveForm))
assert(isinstance(st.agent.mutations[0], ist.MutCondition))
assert(st.agent.mutations[0].residue_from == 'V')
assert(st.agent.mutations[0].residue_to == 'E')
assert(st.agent.mutations[0].position == '600')
assert unicode_strs((tp, st))
assert_if_hgnc_then_up(st)
assert_grounding_value_or_none(st)
assert(st.evidence)
def test_complex_bind():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'The EGFR-EGF complex binds another EGFR-EGF complex.'
tp = trips.process_text(txt, fname, False)
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(is_complex(st))
assert(len(st.members) == 2)
assert(has_hgnc_ref(st.members[0]))
assert(has_hgnc_ref(st.members[1]))
assert(st.members[0].bound_conditions)
assert(st.members[1].bound_conditions)
os.remove(fname)
def test_complex_bind2():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'The EGFR-EGFR complex binds GRB2.'
tp = trips.process_text(txt, fname, False)
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (is_complex(st))
assert (len(st.members) == 2)
assert (st.members[0].name == 'EGFR')
assert (st.members[1].name == 'GRB2')
assert (len(st.members[0].bound_conditions) == 1)
assert (st.members[0].bound_conditions[0].agent.name == 'EGFR')
os.remove(fname)
def test_bound_mod():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'The adaptor protein GRB2 can bind EGFR that is phosphorylated on tyrosine.'
tp = trips.process_text(txt, fname, False)
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (is_complex(st))
assert (len(st.members) == 2)
assert (has_hgnc_ref(st.members[0]))
assert (has_hgnc_ref(st.members[1]))
assert (st.members[1].mods)
assert (st.members[1].mods[0].mod_type == 'phosphorylation')
assert (st.members[1].mods[0].residue == 'Y')
os.remove(fname)
def test_dephosphorylate():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'DUSP6 dephosphorylates ERK2 at Tyr187.'
tp = trips.process_text(txt, fname, False)
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (is_dephosphorylation(st))
assert (st.enz is not None)
assert (st.enz.name == 'DUSP6')
assert (st.sub is not None)
assert (st.sub.name == 'MAPK1')
assert (st.residue == 'Y')
assert (st.position == '187')
os.remove(fname)
def test_transphosphorylate2():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'EGFR, bound to EGFR, transphosphorylates itself on a tyrosine residue.'
tp = trips.process_text(txt, fname, False)
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (is_transphosphorylation(st))
assert (st.enz is not None)
assert (st.enz.name == 'EGFR')
assert (has_hgnc_ref(st.enz))
assert (st.residue == 'Y')
assert (len(st.enz.bound_conditions) == 1)
assert (st.enz.bound_conditions[0].agent.name == 'EGFR')
os.remove(fname)
def test_bound_to3():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'SOS1, bound to GRB2 binds RAS.'
tp = trips.process_text(txt, fname, False)
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (is_complex(st))
assert (len(st.members) == 2)
assert (st.members[0].name == 'SOS1')
assert (has_hgnc_ref(st.members[0]))
assert (st.members[1].name == 'RAS')
assert (len(st.members[0].bound_conditions) == 1)
assert (st.members[0].bound_conditions[0].agent.name == 'GRB2')
os.remove(fname)
def test_bound_mod():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'The adaptor protein GRB2 can bind EGFR that is phosphorylated on tyrosine.'
tp = trips.process_text(txt, fname, False)
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(is_complex(st))
assert(len(st.members) == 2)
assert(has_hgnc_ref(st.members[0]))
assert(has_hgnc_ref(st.members[1]))
assert(st.members[1].mods)
assert(st.members[1].mods[0].mod_type == 'phosphorylation')
assert(st.members[1].mods[0].residue == 'Y')
os.remove(fname)
def test_transphosphorylate2():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'EGFR, bound to EGFR, transphosphorylates itself on a tyrosine residue.'
tp = trips.process_text(txt, fname, False)
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(is_transphosphorylation(st))
assert(st.enz is not None)
assert(st.enz.name == 'EGFR')
assert(has_hgnc_ref(st.enz))
assert(st.residue == 'Y')
assert(len(st.enz.bound_conditions) == 1)
assert(st.enz.bound_conditions[0].agent.name == 'EGFR')
os.remove(fname)
def test_bound_to3():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'SOS1, bound to GRB2 binds RAS.'
tp = trips.process_text(txt, fname, False)
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(is_complex(st))
assert(len(st.members) == 2)
assert(st.members[0].name == 'SOS1')
assert(has_hgnc_ref(st.members[0]))
assert(st.members[1].name == 'RAS')
assert(len(st.members[0].bound_conditions) == 1)
assert(st.members[0].bound_conditions[0].agent.name == 'GRB2')
os.remove(fname)
def test_dephosphorylate():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'DUSP6 dephosphorylates ERK2 at Tyr187.'
tp = trips.process_text(txt, fname, False)
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(is_dephosphorylation(st))
assert(st.enz is not None)
assert(st.enz.name == 'DUSP6')
assert(st.sub is not None)
assert(st.sub.name == 'MAPK1')
assert(st.residue == 'Y')
assert(st.position == '187')
os.remove(fname)
def test_act_mod():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'MEK1, phosphorylated at Ser218 and Ser222, is activated.'
tp = trips.process_text(txt, fname, False)
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (is_actmod(st))
assert (st.agent is not None)
assert (st.agent.name == 'MAP2K1')
residues = [m.residue for m in st.agent.mods]
positions = [m.position for m in st.agent.mods]
assert (residues == ['S', 'S'])
assert (positions == ['218', '222'])
assert (st.is_active)
os.remove(fname)
def test_mod_cond():
tp = trips.process_text('Phosphorylated BRAF binds ubiquitinated MAP2K1.')
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(isinstance(st, ist.Complex))
braf = st.members[0]
mek = st.members[1]
assert(len(braf.mods) == 1)
assert(braf.mods[0].mod_type == 'phosphorylation')
assert(len(mek.mods) == 1)
assert(mek.mods[0].mod_type == 'ubiquitination')
assert unicode_strs((tp, st))
assert_if_hgnc_then_up(st)
assert_grounding_value_or_none(st)
assert(st.evidence)
def test_mod_cond():
tp = trips.process_text('Phosphorylated BRAF binds ubiquitinated MAP2K1.')
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (isinstance(st, ist.Complex))
braf = st.members[0]
mek = st.members[1]
assert (len(braf.mods) == 1)
assert (braf.mods[0].mod_type == 'phosphorylation')
assert (len(mek.mods) == 1)
assert (mek.mods[0].mod_type == 'ubiquitination')
assert unicode_strs((tp, st))
assert_if_hgnc_then_up(st)
assert_grounding_value_or_none(st)
assert (st.evidence)
def test_act_mod():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'MEK1, phosphorylated at Ser218 and Ser222, is activated.'
tp = trips.process_text(txt, fname, False)
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(is_actmod(st))
assert(st.agent is not None)
assert(st.agent.name == 'MAP2K1')
residues = [m.residue for m in st.agent.mods]
positions = [m.position for m in st.agent.mods]
assert(residues == ['S', 'S'])
assert(positions == ['218', '222'])
assert(st.is_active)
os.remove(fname)
def test_not_bound_to():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'BRAF that is not bound to Vemurafenib binds MEK1.'
tp = trips.process_text(txt, fname, False)
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(is_complex(st))
assert(len(st.members) == 2)
assert(st.members[0].name == 'BRAF')
assert(has_hgnc_ref(st.members[0]))
assert(st.members[1].name == 'MAP2K1')
assert(has_hgnc_ref(st.members[1]))
assert(len(st.members[0].bound_conditions) == 1)
assert(st.members[0].bound_conditions[0].agent.name.lower() == 'vemurafenib')
assert(st.members[0].bound_conditions[0].is_bound == False)
os.remove(fname)
def test_not_bound_to():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'BRAF that is not bound to Vemurafenib binds MEK1.'
tp = trips.process_text(txt, fname, False)
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (is_complex(st))
assert (len(st.members) == 2)
assert (st.members[0].name == 'BRAF')
assert (has_hgnc_ref(st.members[0]))
assert (st.members[1].name == 'MAP2K1')
assert (has_hgnc_ref(st.members[1]))
assert (len(st.members[0].bound_conditions) == 1)
assert (
st.members[0].bound_conditions[0].agent.name.lower() == 'vemurafenib')
assert (st.members[0].bound_conditions[0].is_bound == False)
os.remove(fname)
def test_not_bound_to2():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'BRAF, not bound to Vemurafenib, phosphorylates MEK1.'
tp = trips.process_text(txt, fname, False)
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (is_phosphorylation(st))
assert (st.enz is not None)
assert (st.sub is not None)
assert (st.enz.name == 'BRAF')
assert (has_hgnc_ref(st.enz))
assert (st.sub.name == 'MAP2K1')
assert (has_hgnc_ref(st.sub))
assert (len(st.enz.bound_conditions) == 1)
assert (st.enz.bound_conditions[0].agent.name.lower() == 'vemurafenib')
assert (st.enz.bound_conditions[0].is_bound == False)
os.remove(fname)
def test_not_bound_to2():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'BRAF, not bound to Vemurafenib, phosphorylates MEK1.'
tp = trips.process_text(txt, fname, False)
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(is_phosphorylation(st))
assert(st.enz is not None)
assert(st.sub is not None)
assert(st.enz.name == 'BRAF')
assert(has_hgnc_ref(st.enz))
assert(st.sub.name == 'MAP2K1')
assert(has_hgnc_ref(st.sub))
assert(len(st.enz.bound_conditions) == 1)
assert(st.enz.bound_conditions[0].agent.name.lower() == 'vemurafenib')
assert(st.enz.bound_conditions[0].is_bound == False)
os.remove(fname)
def process_trips(txt, reread=True):
print('Using TRIPS')
ts = time.time()
if reread:
stmts = []
sentences = txt.strip().split('\n')
for sentence in sentences:
print(sentence)
tp = trips.process_text(sentence)
stmts += tp.statements
else:
tp = trips.process_xml(open('trips_output.xml', 'r').read())
stmts = tp.statements
te = time.time()
print('Time taken: %.2fs' % (te - ts))
for st in stmts:
print('%s\t%s' % (st, st.evidence[0].text))
return stmts
def assemble_model(model_name, reread=False):
xml_fname = model_name + '.xml'
if not reread:
print('Processing %s' % xml_fname)
if os.path.exists(xml_fname):
with open(xml_fname, 'rb') as fh:
tp = trips.process_xml(fh.read())
else:
reread = True
if reread:
fname = model_name + '.txt'
print('Reading %s' % fname)
with open(fname, 'rb') as fh:
ts = time.time()
tp = trips.process_text(fh.read(), xml_fname)
te = time.time()
print('Reading took %.2fs' % (te - ts))
print('Assembling statements:')
for i, st in enumerate(tp.statements):
print('%d: %s' % (i, st))
print('----------------------')
pa = PysbAssembler()
pa.add_statements(tp.statements)
ts = time.time()
model = pa.make_model()
te = time.time()
print('Assembly took %.2fs' % (te - ts))
model.name = model_name
add_observable(model)
set_parameters(model)
# Save and return model
pa.model = model
pa.save_model('%s.py' % model_name)
return model
def remove_mechanism(text, user_name):
global stmts
import ipdb
ipdb.set_trace()
tp = trips.process_text(text)
gmapper = gm.GroundingMapper(gm.default_grounding_map)
tp_stmts = gmapper.map_agents(tp.statements)
print "Statements to remove:", tp.statements
stmts_to_keep = []
for model_stmt in stmts:
remove_stmt = False
for stmt_to_remove in tp_stmts:
if model_stmt.refinement_of(stmt_to_remove, hierarchies):
remove_stmt = True
break
if not remove_stmt:
stmts_to_keep.append(model_stmt)
if stmts_to_keep == stmts:
say("Sorry, I couldn't find any matching mechanisms to remove.")
else:
say("OK, I removed it.")
stmts = stmts_to_keep
assemble_model(user_name)
def assemble_model(model_id, reread=False):
model_name = 'model%d' % model_id
# If model has already been read, just process the EKB XML
if os.path.exists(model_name + '.xml') and not reread:
tp = trips.process_xml(open(model_name + '.xml').read())
else:
# Start with the basic model
model_txt = open('model1.txt').read()
# Apply patches one by one to get to the current model text
for j in range(1, model_id):
patch_txt = open('model%d_from%d.txt' % (j + 1, j)).read()
model_txt = apply_patch(model_txt, patch_txt)
print('Reading model %d text:' % model_id)
print(model_txt)
# Process model text and save result EKB XML
tp = trips.process_text(model_txt, model_name + '.xml')
print('Assembling statements:')
for i, st in enumerate(tp.statements):
print('%d: %s' % (i, st))
# Assemble the PySB model
pa = PysbAssembler()
pa.add_statements(tp.statements)
model = pa.make_model(policies='two_step')
# Set initial conditions
erk = model.monomers['ERK']
obs = Observable(b'ERK_p', erk(phospho='p'))
model.add_component(obs)
vem = model.monomers['VEMURAFENIB']
obs = Observable(b'Vem_free', vem(map3k=None))
model.add_component(obs)
ras = model.monomers['RAS']
obs = Observable(b'RAS_active', ras(gtp=ANY))
model.add_component(obs)
braf = model.monomers['BRAF']
obs = Observable(b'BRAF_active', braf(vemurafenib=None))
model.add_component(obs)
model.parameters[b'BRAF_0'].value = 0
egf = model.monomers['EGF']
obs = Observable(b'EGF_free', egf(erbb=None))
model.add_component(obs)
# Add mutated form of BRAF as initial condition
sites_dict = {}
for site in braf.sites:
if site in braf.site_states:
sites_dict[site] = braf.site_states[site][0]
else:
sites_dict[site] = None
sites_dict['V600'] = 'E'
model.add_component(Parameter('BRAF_mut_0', 1e5))
model.initial(braf(**sites_dict), model.parameters['BRAF_mut_0'])
# Set up model parameters
model.parameters['kf_ee_bind_1'].value = 1
model.parameters['kr_ee_bind_1'].value = 0.1
model.parameters['kf_ee_bind_2'].value = 1
model.parameters['kr_ee_bind_2'].value = 0.1
model.parameters['kf_eg_bind_1'].value = 1
model.parameters['kr_eg_bind_1'].value = 0.1
model.parameters['kf_gs_bind_1'].value = 1
model.parameters['kr_gs_bind_1'].value = 0.1
model.parameters['kf_sr_bind_1'].value = 1
model.parameters['kr_sr_bind_1'].value = 50
model.parameters['kf_rg_bind_1'].value = 50
model.parameters['kr_rg_bind_1'].value = 0.5
model.parameters['kf_rb_bind_1'].value = 1
model.parameters['kr_rb_bind_1'].value = 0.5
model.parameters['kf_vb_bind_1'].value = 10
model.parameters['kr_vb_bind_1'].value = 1
model.parameters['kf_bm_bind_1'].value = 1
model.parameters['kr_bm_bind_1'].value = 0.1
model.parameters['kc_bm_phosphorylation_1'].value = 3
model.parameters['kf_pm_bind_1'].value = 1
model.parameters['kr_pm_bind_1'].value = 0.001
model.parameters['kc_pm_dephosphorylation_1'].value = 10
model.parameters['kf_me_bind_1'].value = 1
model.parameters['kr_me_bind_1'].value = 0.1
model.parameters['kc_me_phosphorylation_1'].value = 10
model.parameters['kf_de_bind_1'].value = 1
model.parameters['kr_de_bind_1'].value = 0.001
model.parameters['kc_de_dephosphorylation_1'].value = 10
model.parameters['VEMURAFENIB_0'].value = 0
model.parameters['EGF_0'].value = 1e3
model.parameters['EGFR_0'].value = 1e5
model.parameters['SOS_0'].value = 1e3
model.parameters['GRB2_0'].value = 1e5
model.parameters['RAS_0'].value = 2e5
model.parameters['GTP_0'].value = 1e7
model.parameters['MEK_0'].value = 1e5
model.parameters['ERK_0'].value = 1e5
model.parameters['DUSP6_0'].value = 1e3
model.parameters['PPP2CA_0'].value = 1e5
if model_id >= 2:
model.parameters['Phosphatase_0'].value = 1e2
model.parameters['kf_es_bind_1'].value = 1e-05
model.parameters['kr_es_bind_1'].value = 1e-04
model.parameters['kc_es_phosphorylation_1'].value = 1
model.parameters['kf_ps_bind_1'].value = 1
model.parameters['kr_ps_bind_1'].value = 0.1
model.parameters['kc_ps_dephosphorylation_1'].value = 1e-04
if model_id >= 3:
model.parameters['kf_bb_bind_1'].value = 10
model.parameters['kr_bb_bind_1'].value = 1
model.parameters['kf_vb_bind_2'].value = 1e-04
pa.model = model
pa.save_model('model%d.py' % model_id)
return model
def test_trips_processor_online():
"""Smoke test to see if imports and executes without error. Doesn't
check for correctness of parse or of assembled model."""
tp = trips.process_text('BRAF phosphorylates MEK1 at Ser222.')
def make_ekb(txt):
fname = re.sub('[^a-zA-Z0-9]', '_', txt[:-1]) + '.ekb'
tp = trips.process_text(txt, save_xml_name=fname)
print(txt)
print(tp.statements)
import numpy as np
from pysb.integrate import Solver
from matplotlib import pyplot as plt
from indra import bel, biopax, trips
from indra.util import plot_formatting as pf
from indra.assemblers import PysbAssembler
# 1. TEXT
# User defines text:
text = ('MEK1 phosphorylates ERK2 on threonine 185 and tyrosine 187.')
# Show round trip going out to TRIPS/DRUM web service,
# return logical form to INDRA, which is queried by
# INDRA for relevant statements
tp = trips.process_text(text)
# Now generate PySB model
stmts = tp.statements # Don't show this one
pa = PysbAssembler()
pa.add_statements(stmts)
pa.make_model()
t = np.linspace(0, 25000)
sol = Solver(pa.model, t)
sol.run()
pf.set_fig_params()
plt.ion()
plt.figure(figsize=(1, 1), dpi=300)
species_names = [str(s) for s in pa.model.species]
plt.plot(t, sol.y[:, species_names.index("MAPK1(T185='u', Y187='u')")],
import numpy as np
from pysb.integrate import Solver
from matplotlib import pyplot as plt
from indra import bel, biopax, trips
from indra.util import plot_formatting as pf
from indra.assemblers import PysbAssembler
# 1. TEXT
# User defines text:
text = ('MEK1 phosphorylates ERK2 on threonine 185 and tyrosine 187.')
# Show round trip going out to TRIPS/DRUM web service,
# return logical form to INDRA, which is queried by
# INDRA for relevant statements
tp = trips.process_text(text)
# Now generate PySB model
stmts = tp.statements # Don't show this one
pa = PysbAssembler()
pa.add_statements(stmts)
pa.make_model()
t = np.linspace(0, 25000)
sol = Solver(pa.model, t)
sol.run()
pf.set_fig_params()
plt.ion()
plt.figure(figsize=(1, 1), dpi=300)
species_names = [str(s) for s in pa.model.species]
plt.plot(t,
def update_model_from_text(text, requester_name):
global stmts
say("%s: Got it. Assembling model..." % requester_name)
tp = trips.process_text(text)
stmts += tp.statements
assemble_model(requester_name)
