def summarize(self):
summary = {
'stmt_types':
[statement_base_verb(v) for v in self.get_stmt_types()],
'query_subj': self.query.subj,
'query_obj': self.query.obj
}
return summary
def summarize(self):
if self.query.stmt_type:
stmt_type = statement_base_verb(self.query.stmt_type.lower())
else:
stmt_type = None
summary = {'stmt_type': stmt_type,
'query_subj': self.query.subj,
'other_agents': self.get_other_agents([self.query.subj],
other_role='object')}
return summary
def to_english(self):
agent = _assemble_agent_str(self.entity).agent_str
if self.entity_role == 'subject':
verb = statement_base_verb(self.stmt_type.lower())
verb = verb[0].lower() + verb[1:]
sentence = f'What does {agent} {verb}?'
elif self.entity_role == 'object':
verb = statement_present_verb(self.stmt_type.lower())
verb = verb[0].lower() + verb[1:]
sentence = f'What {verb} {agent}?'
sentence = sentence[0].upper() + sentence[1:]
if self.terminal_ns:
sentence += f' ({", ".join(self.terminal_ns).upper()})'
return sentence
def _build_verb_map():
# We first get all statement types
stmts = get_all_descendants(Statement)
verb_map = {}
# These are statement types that aren't binary and therefore don't need
# to be included in the verb map
non_binary = ('hasactivity', 'activeform', 'selfmodification',
'autophosphorylation', 'transphosphorylation', 'event',
'unresolved', 'association', 'complex')
for stmt in stmts:
# Get the class name
name = stmt.__name__
if name.lower() in non_binary:
continue
# Get the base verb form of the statement, e.g., "phosphorylate"
base_verb = statement_base_verb(name.lower())
verb_map[base_verb] = {'stmt': name, 'type': 'base'}
# Get the present form of the statement, e.g., "inhibits"
present_verb = statement_present_verb(name.lower())
verb_map[present_verb] = {'stmt': name, 'type': 'present'}
# Get the passive / state form of the statement, e.g., "activated"
passive_verb = statement_passive_verb(name.lower())
verb_map[passive_verb] = {'stmt': name, 'type': 'passive'}
return verb_map
def test_get_base_verb():
assert ea.statement_base_verb('inhibition') == 'inhibit'
assert ea.statement_base_verb('dephosphorylation') == 'dephosphorylate'
assert ea.statement_base_verb('complex') == 'bind'