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)
# 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)
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)
import sys
import csv
import shutil
import pickle
from indra.sources import reach
from indra.util import read_unicode_csv
from indra.literature import pmc_client, get_full_text, id_lookup
from assembly_eval import have_file, run_assembly
if __name__ == '__main__':
# This script assumes that the papers have been processed offline,
# e.g., using the submit_reading_pipeline.py script on Amazon,
# and the results placed in a dict (mapping PMID -> lists of statements)
# and put in the folder reach/reach_stmts_batch_4_eval.pkl.
folder = 'reach'
# Load the PMID to PMCID map
pmid_to_pmcid = {}
csvreader = read_unicode_csv('pmc_batch_4_id_map.txt', delimiter='\t')
for row in csvreader:
pmid_to_pmcid[row[1]] = row[0]
# Load the REACH reading output
with open(os.path.join(folder, 'reach_stmts_batch_4_eval.pkl'), 'rb') as f:
stmts = pickle.load(f)
# Iterate over all of the PMIDs
for pmid, stmts in stmts.items():
pmcid = pmid_to_pmcid[pmid]
run_assembly(stmts, folder, pmcid)
if __name__ == '__main__':
pmc_ids = [s.strip() for s in open('pmcids.txt', 'rt').readlines()]
# 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
# Run assembly
run_assembly(all_statements, 'combined', pmcid,
background_assertions=rasmodel_stmts)
reach_stmts = pickle.load(f)
# Load the PMID to PMCID map
pmcid_to_pmid = {}
with open('pmc_batch_4_id_map.txt') as f:
csvreader = csv.reader(f, 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 NACTEM/ISI statements
fname = 'nactem/' + pmcid + '.cards'
if not os.path.exists(fname):
nactem_stmts = []
else:
icp = index_cards.process_json_file(fname, 'nactem')
nactem_stmts = icp.statements
# Combine all statements
all_statements = tp.statements + reach_stmts_for_pmcid + nactem_stmts
# Run assembly
run_assembly(all_statements, 'combined', pmcid)
from __future__ import absolute_import, print_function, unicode_literals
from builtins import dict, str
from indra.sources 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)
