def run_assembly(self):
"""Run INDRA's assembly pipeline on the Statements."""
self.eliminate_copies()
stmts = self.get_indra_stmts()
stmts = self.filter_event_association(stmts)
stmts = ac.filter_no_hypothesis(stmts)
if not self.assembly_config.get('skip_map_grounding'):
stmts = ac.map_grounding(stmts)
if self.assembly_config.get('standardize_names'):
ac.standardize_names_groundings(stmts)
if self.assembly_config.get('filter_ungrounded'):
score_threshold = self.assembly_config.get('score_threshold')
stmts = ac.filter_grounded_only(stmts,
score_threshold=score_threshold)
if self.assembly_config.get('merge_groundings'):
stmts = ac.merge_groundings(stmts)
if self.assembly_config.get('merge_deltas'):
stmts = ac.merge_deltas(stmts)
relevance_policy = self.assembly_config.get('filter_relevance')
if relevance_policy:
stmts = self.filter_relevance(stmts, relevance_policy)
if not self.assembly_config.get('skip_filter_human'):
stmts = ac.filter_human_only(stmts)
if not self.assembly_config.get('skip_map_sequence'):
stmts = ac.map_sequence(stmts)
# Use WM hierarchies and belief scorer for WM preassembly
preassembly_mode = self.assembly_config.get('preassembly_mode')
if preassembly_mode == 'wm':
hierarchies = get_wm_hierarchies()
belief_scorer = get_eidos_scorer()
stmts = ac.run_preassembly(stmts,
return_toplevel=False,
belief_scorer=belief_scorer,
hierarchies=hierarchies)
else:
stmts = ac.run_preassembly(stmts, return_toplevel=False)
belief_cutoff = self.assembly_config.get('belief_cutoff')
if belief_cutoff is not None:
stmts = ac.filter_belief(stmts, belief_cutoff)
stmts = ac.filter_top_level(stmts)
if self.assembly_config.get('filter_direct'):
stmts = ac.filter_direct(stmts)
stmts = ac.filter_enzyme_kinase(stmts)
stmts = ac.filter_mod_nokinase(stmts)
stmts = ac.filter_transcription_factor(stmts)
if self.assembly_config.get('mechanism_linking'):
ml = MechLinker(stmts)
ml.gather_explicit_activities()
ml.reduce_activities()
ml.gather_modifications()
ml.reduce_modifications()
ml.gather_explicit_activities()
ml.replace_activations()
ml.require_active_forms()
stmts = ml.statements
self.assembled_stmts = stmts
def reground_tests(tests, webservice):
"""Reground tests to updated ontology."""
stmts = [test.stmt for test in tests]
texts = [stmt.evidence[0].text for stmt in stmts]
text = ' '.join(texts)
new_stmts = process_text(text, webservice=webservice).statements
new_stmts = standardize_names_groundings(new_stmts)
new_tests = [StatementCheckingTest(stmt) for stmt in new_stmts]
return new_tests
def default_assembly(stmts):
from indra.belief.wm_scorer import get_eidos_scorer
from indra.preassembler.hierarchy_manager import get_wm_hierarchies
hm = get_wm_hierarchies()
scorer = get_eidos_scorer()
stmts = ac.run_preassembly(stmts, belief_scorer=scorer,
return_toplevel=True,
flatten_evidence=True,
flatten_evidence_collect_from='supported_by',
poolsize=4)
stmts = ac.merge_groundings(stmts)
stmts = ac.merge_deltas(stmts)
stmts = ac.standardize_names_groundings(stmts)
return stmts
def default_assembly(stmts):
from indra.belief.wm_scorer import get_eidos_scorer
from indra.preassembler.hierarchy_manager import get_wm_hierarchies
hm = get_wm_hierarchies()
scorer = get_eidos_scorer()
stmts = ac.run_preassembly(stmts, belief_scorer=scorer,
return_toplevel=True,
flatten_evidence=True,
flatten_evidence_collect_from='supported_by',
poolsize=4)
stmts = ac.merge_groundings(stmts)
stmts = ac.merge_deltas(stmts)
stmts = ac.standardize_names_groundings(stmts)
return stmts
from indra.tools import assemble_corpus as ac
from indra.sources.eidos import migration_table_processor as mtp
from indra.preassembler.hierarchy_manager import YamlHierarchyManager
from indra.preassembler.make_eidos_hume_ontologies import load_yaml_from_url, \
rdf_graph_from_yaml
from indra.preassembler.custom_preassembly import location_time_delta_matches, \
location_time_delta_refinement
from indra.belief.wm_scorer import get_eidos_scorer
wm_ont_url = ('https://raw.githubusercontent.com/WorldModelers/'\
'Ontologies/master/wm.yml')
if __name__ == '__main__':
fname = 'grounded CAG links - New Ontology.xlsx'
stmts = mtp.process_workbook(fname)
hm = YamlHierarchyManager(load_yaml_from_url(wm_ont_url),
rdf_graph_from_yaml, True)
stmts = ac.run_preassembly(stmts,
return_toplevel=False,
belief_score=get_eidos_scorer(),
hierarchies={'entity': hm},
matches_fun=location_time_delta_matches,
refinement_fun=location_time_delta_refinement)
stmts = ac.standardize_names_groundings(stmts)