def process_sentence_xml(sentence):
fname = re.sub('[^a-zA-Z0-9]', '_', sentence[:-1]) + '.ekb'
path = os.path.join(path_this, 'trips_ekbs', fname)
with open(path, 'rb') as fh:
xml = fh.read().decode('utf-8')
tp = trips.process_xml(xml)
return tp
def get_file_stmts(fname):
with open(fname, 'rt') as fh:
xml_str = fh.read()
tp = trips.process_xml(xml_str)
if tp is None:
return []
return tp.statements
def process_sentence_xml(sentence):
fname = re.sub('[^a-zA-Z0-9]', '_', sentence[:-1]) + '.ekb'
path = os.path.join(path_this, 'trips_ekbs', fname)
with open(path, 'rb') as fh:
xml = fh.read().decode('utf-8')
tp = trips.process_xml(xml)
return tp
def get_file_stmts(fname):
with open(fname, 'rt') as fh:
xml_str = fh.read()
tp = trips.process_xml(xml_str)
if tp is None:
return []
return tp.statements
def trips_process_xml():
"""Process TRIPS EKB XML and return INDRA Statements."""
response = request.body.read().decode('utf-8')
body = json.loads(response)
xml_str = body.get('xml_str')
tp = trips.process_xml(xml_str)
if tp and tp.statements:
stmts = stmts_to_json(tp.statements)
res = {'statements': stmts}
return res
else:
res = {'statements': []}
return res
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
from __future__ import absolute_import, print_function, unicode_literals
from builtins import dict, str
from indra import trips
from assembly_eval import have_file, run_assembly
if __name__ == '__main__':
pmc_ids = [s.strip() for s in open('pmcids.txt', 'rt').readlines()]
# Use the existing EKB extractions.
for pmcid in pmc_ids:
folder = 'trips'
prefix = folder + '/' + pmcid
print('Processing %s...' % pmcid)
with open(prefix + '.ekb', 'r') as f:
tp = trips.process_xml(f.read())
# PMIDs from TRIPS need to be set here because it propagates
# the PMCID by default
run_assembly(tp.statements, folder, pmcid)
# Load the REACH reading output
with open('reach/reach_stmts_batch_4_eval.pkl', 'rb') as f:
reach_stmts = pickle.load(f)
# Load the PMID to PMCID map
pmcid_to_pmid = {}
csvreader = read_unicode_csv('pmc_batch_4_id_map.txt', delimiter='\t')
for row in csvreader:
pmcid_to_pmid[row[0]] = row[1]
for pmcid in pmc_ids:
print('Processing %s...' % pmcid)
# Process TRIPS
trips_fname = 'trips/' + pmcid + '.ekb'
tp = trips.process_xml(open(trips_fname).read())
# Get REACH statements
reach_stmts_for_pmcid = reach_stmts.get(pmcid_to_pmid[pmcid], [])
if not reach_stmts_for_pmcid:
print("No REACH statements for %s" % pmcid)
# Get prior statements
rasmodel_stmts = rasmodel.get_statements()
# Combine all statements
all_statements = tp.statements + reach_stmts_for_pmcid
for stmt in all_statements:
stmt.uuid = str(uuid.uuid4())
# Run assembly
run_assembly(all_statements,
'combined',
pmcid,
background_assertions=rasmodel_stmts)
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
from indra import trips
from indra.literature import id_lookup
from assembly_eval import have_file, run_assembly
if __name__ == '__main__':
pmc_ids = ['PMC1234335', 'PMC3178447', 'PMC3690480',
'PMC4345513', 'PMC534114']
pmids = [id_lookup(pmcid)['pmid'] for pmcid in pmc_ids]
# Use the existing EKB extractions.
for pmid, pmcid in zip(pmids, pmc_ids):
folder = 'trips'
prefix = folder + '/' + pmcid
print 'Processing %s...' % pmcid
tp = trips.process_xml(open(prefix + '-20160503T1152.ekb').read())
# PMIDs from TRIPS need to be set here because it propagates
# the PMCID by default
for s in tp.statements:
for e in s.evidence:
e.pmid = pmid
run_assembly(tp.statements, folder, pmcid)
from indra import trips, reach
from indra.literature import id_lookup
from assembly_eval import have_file, run_assembly
if __name__ == "__main__":
pmc_ids = ["PMC1234335", "PMC3178447", "PMC3690480", "PMC4345513", "PMC534114"]
pmids = [id_lookup(pmcid)["pmid"] for pmcid in pmc_ids]
for pmid, pmcid in zip(pmids, pmc_ids):
print "Processing %s..." % pmcid
trips_fname = "trips/" + pmcid + "-20160503T1152.ekb"
tp = trips.process_xml(open(trips_fname).read())
for s in tp.statements:
for e in s.evidence:
e.pmid = pmid
reach_fname = "reach/" + pmcid + ".json"
rp = reach.process_json_file(reach_fname)
all_statements = tp.statements + rp.statements
run_assembly(all_statements, "combined", pmcid)
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:
tp = trips.process_text(fh.read(), xml_fname)
print('Assembling statements:')
for i, st in enumerate(tp.statements):
print('%d: %s' % (i, st))
print('----------------------')
pa = PysbAssembler()
pa.add_statements(tp.statements)
model = pa.make_model()
model.name = model_name
p53 = model.monomers['TP53']
obs = Observable(b'p53_active', p53(activity='active'))
model.add_component(obs)
if not model_name.endswith('var'):
model.parameters['kf_aa_act_1'].value = 5e-06
model.parameters['kf_pt_act_1'].value = 1e-05
if model_name == 'p53_ATM':
model.add_component(Parameter('ATMa_0', 1))
atm = model.monomers['ATM']
model.initial(atm(activity='active'), model.parameters['ATMa_0'])
model.parameters['kf_pa_act_1'].value = 1e-04
obs = Observable(b'atm_active', atm(activity='active'))
model.add_component(obs)
if model_name == 'p53_ATR':
model.add_component(Parameter('ATRa_0', 1))
atr = model.monomers['ATR']
model.initial(atr(activity='active'), model.parameters['ATRa_0'])
obs = Observable(b'atr_active', atr(activity='active'))
model.add_component(obs)
if model_name == 'p53_ATM_var':
#model.add_component(Parameter('ATMa_0', 1))
#atm = model.monomers['ATM']
#model.initial(atm(activity='active'),
# model.parameters['ATMa_0'])
model.add_component(Parameter('ATMa_0', 1))
atm = model.monomers['ATM']
model.initial(atm(phospho='p'), model.parameters['ATMa_0'])
model.parameters['kf_pa_dephosphorylation_1'].value = 1e-04
model.parameters['MDM2_0'].value = 0
model.parameters['kf_m_deg_1'].value = 8e-01
model.parameters['kf_tm_synth_1'].value = 0.2
model.parameters['kf_aa_phosphorylation_1'].value = 5e-06
obs = Observable(b'atm_active', atm(phospho='p'))
model.add_component(obs)
pa.model = model
pa.save_model('%s.py' % model_name)
return model
from indra import trips
from indra.literature import id_lookup
from assembly_eval import have_file, run_assembly
if __name__ == '__main__':
pmc_ids = [s.strip() for s in open('pmcids.txt', 'rt').readlines()]
pmids = [id_lookup(pmcid)['pmid'] for pmcid in pmc_ids]
# Use the existing EKB extractions.
for pmid, pmcid in zip(pmids, pmc_ids):
folder = 'trips'
prefix = folder + '/' + pmcid
print 'Processing %s...' % pmcid
tp = trips.process_xml(open(prefix + '_20160614.ekb').read())
# PMIDs from TRIPS need to be set here because it propagates
# the PMCID by default
for s in tp.statements:
for e in s.evidence:
e.pmid = pmid
run_assembly(tp.statements, folder, pmcid)
def test_trips_processor_offline():
"""Smoke test to see if imports and executes without error. Doesn't
check for correctness of parse or of assembled model."""
tp = trips.process_xml(open(test_small_file).read())
db_refs_str = ', '.join(db_refs)
ev_txt = (s.evidence[0].text).encode('utf-8')
fh.write('%s\t%s\t%s\t%s\n' %
(s, db_refs_str, 'PMC'+s.evidence[0].pmid,
ev_txt))
if __name__ == '__main__':
fnames = glob.glob('*.ekb')
pa = Preassembler(eh, mh)
for fn in fnames:
print '\n\n----------------------------'
print 'Processing %s...' % fn
xml_str = open(fn, 'rt').read()
tp = trips.process_xml(xml_str)
print 'Extracted events by type'
print '------------------------'
for k,v in tp.extracted_events.iteritems():
print k, len(v)
print '------------------------'
print '%s statements collected.' % len(tp.statements)
pa.add_statements(tp.statements)
print '----------------------------\n\n'
print '%d statements collected in total.' % len(pa.stmts)
duplicate_stmts = pa.combine_duplicates()
print '%d statements after combining duplicates.' % len(duplicate_stmts)
related_stmts = pa.combine_related()
print '%d statements after combining related.' % len(related_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:
tp = trips.process_text(fh.read(), xml_fname)
print('Assembling statements:')
for i, st in enumerate(tp.statements):
print('%d: %s' % (i, st))
print('----------------------')
pa = PysbAssembler()
pa.add_statements(tp.statements)
model = pa.make_model()
model.name = model_name
p53 = model.monomers['TP53']
obs = Observable(b'p53_active', p53(activity='active'))
model.add_component(obs)
if not model_name.endswith('var'):
model.parameters['kf_aa_act_1'].value = 5e-06
model.parameters['kf_pt_act_1'].value = 1e-05
if model_name == 'p53_ATM':
model.add_component(Parameter('ATMa_0', 1))
atm = model.monomers['ATM']
model.initial(atm(activity='active'),
model.parameters['ATMa_0'])
model.parameters['kf_pa_act_1'].value = 1e-04
obs = Observable(b'atm_active', atm(activity='active'))
model.add_component(obs)
if model_name == 'p53_ATR':
model.add_component(Parameter('ATRa_0', 1))
atr = model.monomers['ATR']
model.initial(atr(activity='active'),
model.parameters['ATRa_0'])
obs = Observable(b'atr_active', atr(activity='active'))
model.add_component(obs)
if model_name == 'p53_ATM_var':
#model.add_component(Parameter('ATMa_0', 1))
#atm = model.monomers['ATM']
#model.initial(atm(activity='active'),
# model.parameters['ATMa_0'])
model.add_component(Parameter('ATMa_0', 1))
atm = model.monomers['ATM']
model.initial(atm(phospho='p'),
model.parameters['ATMa_0'])
model.parameters['kf_pa_dephosphorylation_1'].value = 1e-04
model.parameters['MDM2_0'].value = 0
model.parameters['kf_m_deg_1'].value = 8e-01
model.parameters['kf_tm_synth_1'].value = 0.2
model.parameters['kf_aa_phosphorylation_1'].value = 5e-06
obs = Observable(b'atm_active', atm(phospho='p'))
model.add_component(obs)
pa.model = model
pa.save_model('%s.py' % model_name)
return model