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_api.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_bind():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'The receptor tyrosine kinase EGFR binds the growth factor ligand EGF.'
tp = trips_api.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_complex_bind2():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'RAF binds to the RAS-GTP complex.'
tp = trips_api.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_mod():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'The adaptor protein GRB2 can bind EGFR that is phosphorylated on tyrosine.'
tp = trips_api.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 ('PhosphorylationTyrosine' in st.members[1].mods)
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_api.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('PhosphorylationTyrosine' in st.members[1].mods)
os.remove(fname)
def text_to_sbgn(text=None, trips_xml=None):
if (text is None and trips_xml is None) or (text is not None and trips_xml is not None):
raise ValueError("Must provide ONE of 'text' or 'trips_xml'")
elif text is not None:
tp = trips_api.process_text(text)
elif trips_xml is not None:
tp = trips_api.process_xml(trips_xml)
else:
raise RuntimeError("Unexpected or impossible combination of arguments")
sa = SBGNAssembler()
sa.add_statements(tp.statements)
sbgn_output = sa.make_sbgn()
return sbgn_output
def test_bound_phosphorylate():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'RAF, bound to RAF, phosphorylates MEK1.'
tp = trips_api.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.mod == 'Phosphorylation')
os.remove(fname)
def test_complex_bind2():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'RAF binds to the RAS-GTP complex.'
tp = trips_api.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_act_mod():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'MEK1, phosphorylated at Ser218 and Ser222, is activated.'
tp = trips_api.process_text(txt, fname, False)
assert(len(tp.statements) == 1)
st = tp.statements[0]
assert(is_actmod(st))
assert(st.monomer is not None)
assert(st.monomer.name == 'MAP2K1')
assert(st.monomer.mod == ['PhosphorylationSerine', 'PhosphorylationSerine'])
assert(st.monomer.mod_pos == ['218', '222'])
assert(st.relationship == 'increases')
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_api.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_bound_phosphorylate():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'RAF, bound to RAF, phosphorylates MEK1.'
tp = trips_api.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.mod == 'Phosphorylation')
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_api.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_transphosphorylate2():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'EGFR, bound to EGFR, transphosphorylates itself on a tyrosine residue.'
tp = trips_api.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.mod == 'PhosphorylationTyrosine')
assert(len(st.enz.bound_conditions) == 1)
assert(st.enz.bound_conditions[0].agent.name == 'EGFR')
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_api.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.mod == 'PhosphorylationTyrosine')
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_api.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_api.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.mod == 'PhosphorylationTyrosine')
assert(st.mod_pos == '187')
os.remove(fname)
def test_bound_to3():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'SOS1, bound to GRB2 binds RAS.'
tp = trips_api.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_api.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.mod == 'PhosphorylationTyrosine')
assert (st.mod_pos == '187')
os.remove(fname)
def text_to_sbgn(text=None, trips_xml=None):
if ((text is None and trips_xml is None)
or (text is not None and trips_xml is not None)):
raise ValueError("Must provide ONE of 'text' or 'trips_xml'")
elif text is not None:
tp = trips_api.process_text(text)
elif trips_xml is not None:
tp = trips_api.process_xml(trips_xml)
else:
raise RuntimeError("Unexpected or impossible combination of arguments")
sa = SBGNAssembler()
sa.add_statements(tp.statements)
sbgn_output = sa.make_model()
return sbgn_output
def test_act_mod():
fname = sys._getframe().f_code.co_name + '.xml'
txt = 'MEK1, phosphorylated at Ser218 and Ser222, is activated.'
tp = trips_api.process_text(txt, fname, False)
assert (len(tp.statements) == 1)
st = tp.statements[0]
assert (is_actmod(st))
assert (st.monomer is not None)
assert (st.monomer.name == 'MAP2K1')
assert (st.monomer.mod == [
'PhosphorylationSerine', 'PhosphorylationSerine'
])
assert (st.monomer.mod_pos == ['218', '222'])
assert (st.relationship == 'increases')
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_api.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_api.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_api.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_api.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_trips_processor_online():
"""Smoke test to see if imports and executes without error. Doesn't
check for correctness of parse or of assembled model."""
pa = PysbAssembler()
tp = trips_api.process_text('BRAF phosphorylates MEK1 at Ser222.')
pa.add_statements(tp.statements)
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."""
pa = PysbAssembler()
tp = trips_api.process_text('BRAF phosphorylates MEK1 at Ser222.')
pa.add_statements(tp.statements)
def make_statements(text):
"""Given text, return a list of INDRA statements."""
from indra.trips import trips_api
tp = trips_api.process_text(text)
return tp.statements
def make_statements(text):
"""Given text, return a list of INDRA statements."""
from indra.trips import trips_api
tp = trips_api.process_text(text)
return tp.statements
from indra.biopax import biopax_api
from indra.trips import trips_api
from indra_to_kami import nodes_to_kami, IndraKamiConverter
import indra.statements
import json
# Get a biopax processor from a biopax query
#bp = biopax_api.process_pc_pathsfromto(['BRAF'], ['MAP2K1'])
#bp.get_phosphorylation()
tp = trips_api.process_text('MEK2 phosphorylates ERK1 at Thr-202 and Tyr-204')
ikc = IndraKamiConverter()
nodes = set([])
# Collect the nodes to generate from the INDRA statements
for stmt in tp.statements:
if isinstance(stmt, indra.statements.Phosphorylation):
new_nodes = ikc.phosphorylation(stmt)
nodes.update(new_nodes)
# Create the JSON output
output = nodes_to_kami(nodes)
json_str = json.dumps(output, indent=2)
with open('indra_to_kami_example1.json', 'w') as f:
f.write(json_str)
def make_statements(text):
from indra.trips import trips_api
tp = trips_api.process_text(text)
return tp.statements