def create_message1(self):
txt = 'ELK1 transcribes FOS.'
model = stmts_kstring_from_text(txt)
entity = ekb_kstring_from_text('FOS')
entities = KQMLList([KQMLList([':description', entity])])
pattern = KQMLList()
pattern.set('entities', entities)
pattern.sets('type', 'eventual_value')
value = KQMLList()
value.sets('type', 'qualitative')
value.sets('value', 'high')
pattern.set('value', value)
content = KQMLList('SATISFIES-PATTERN')
content.set('pattern', pattern)
content.set('model', model)
condition_entity = ekb_kstring_from_text('MAPK1')
conditions = KQMLList()
condition = KQMLList()
condition.sets('type', 'multiple')
condition.set('value', '100.0')
quantity = KQMLList()
quantity.sets('type', 'total')
entity = KQMLList()
entity.set('description', condition_entity)
quantity.set('entity', entity)
condition.set('quantity', quantity)
conditions.append(condition)
content.set('conditions', conditions)
msg = get_request(content)
return (msg, content)
def create_message(self):
txt = 'MEK not bound to Selumetinib phosphorylates ERK. DUSP dephosphorylates ERK. ' + \
'Selumetinib binds MEK.'
model = stmts_kstring_from_text(txt)
entity = ekb_kstring_from_text('ERK that is phosphorylated')
entities = KQMLList([KQMLList([':description', entity])])
pattern = KQMLList()
pattern.set('entities', entities)
pattern.sets('type', 'always_value')
value = KQMLList()
value.sets('type', 'qualitative')
value.sets('value', 'low')
pattern.set('value', value)
content = KQMLList('SATISFIES-PATTERN')
content.set('pattern', pattern)
content.set('model', model)
condition_entity = ekb_kstring_from_text('Selumetinib')
conditions = KQMLList()
condition = KQMLList()
condition.sets('type', 'multiple')
condition.set('value', '100.0')
quantity = KQMLList()
quantity.sets('type', 'total')
entity = KQMLList()
entity.set('description', condition_entity)
quantity.set('entity', entity)
condition.set('quantity', quantity)
conditions.append(condition)
content.set('conditions', conditions)
msg = get_request(content)
return (msg, content)
def create_message(self):
model = stmts_kstring_from_text('MAP2K1 binds MAPK1')
entity = ekb_kstring_from_text('MAPK1-MAP2K1 complex')
condition_entity = ekb_kstring_from_text('MAP2K1')
entities = KQMLList([KQMLList([':description', entity])])
pattern = KQMLList()
pattern.set('entities', entities)
pattern.sets('type', 'always_value')
value = KQMLList()
value.sets('type', 'qualitative')
value.sets('value', 'high')
pattern.set('value', value)
content = KQMLList('SATISFIES-PATTERN')
content.set('pattern', pattern)
content.set('model', model)
conditions = KQMLList()
condition = KQMLList()
condition.sets('type', 'multiple')
condition.set('value', '10.0')
quantity = KQMLList()
quantity.sets('type', 'total')
entity = KQMLList()
entity.set('description', condition_entity)
quantity.set('entity', entity)
condition.set('quantity', quantity)
conditions.append(condition)
content.set('conditions', conditions)
msg = get_request(content)
return (msg, content)
def create_message(self):
model = stmts_kstring_from_text('MEK binds ERK')
entity = ekb_kstring_from_text('the MEK-ERK complex')
entities = KQMLList([KQMLList([':description', entity])])
pattern = KQMLList()
pattern.set('entities', entities)
pattern.sets('type', 'always_value')
value = KQMLList()
value.sets('type', 'qualitative')
value.sets('value', 'low')
pattern.set('value', value)
content = KQMLList('SATISFIES-PATTERN')
content.set('pattern', pattern)
content.set('model', model)
msg = get_request(content)
return (msg, content)
def create_message(self):
model = stmts_kstring_from_text('MEK phosphorylates ERK')
entity = ekb_kstring_from_text('ERK that is phosphorylated')
entities = KQMLList([KQMLList([':description', entity])])
pattern = KQMLList()
pattern.set('entities', entities)
pattern.sets('type', 'eventual_value')
value = KQMLList()
value.sets('type', 'qualitative')
value.sets('value', 'high')
pattern.set('value', value)
content = KQMLList('SATISFIES-PATTERN')
content.set('pattern', pattern)
content.set('model', model)
msg = get_request(content)
return (msg, content)
def create_message(self):
txt = 'ELK1 transcribes FOS.'
model = stmts_kstring_from_text(txt)
entity = ekb_kstring_from_text('FOS')
entities = KQMLList([KQMLList([':description', entity])])
pattern = KQMLList()
pattern.set('entities', entities)
pattern.sets('type', 'eventual_value')
value = KQMLList()
value.sets('type', 'qualitative')
value.sets('value', 'high')
pattern.set('value', value)
content = KQMLList('SATISFIES-PATTERN')
content.set('pattern', pattern)
content.set('model', model)
msg = get_request(content)
return (msg, content)
def create_message1(self):
txt = 'MAP2K1 phosphorylates MAPK1.'
model = stmts_kstring_from_text(txt)
entity = ekb_kstring_from_text('MAPK1-bound MAP2K1')
entities = KQMLList([KQMLList([':description', entity])])
pattern = KQMLList()
pattern.set('entities', entities)
pattern.sets('type', 'sustained')
value = KQMLList()
value.sets('type', 'qualitative')
value.sets('value', 'high')
pattern.set('value', value)
content = KQMLList('SATISFIES-PATTERN')
content.set('pattern', pattern)
content.set('model', model)
msg = get_request(content)
return (msg, content)
def __init__(self, *args, **kwargs):
super(TestCompareConditions, self).__init__(tra_module.TRA_Module,
use_kappa=False)
model_txt = 'Vemurafenib inhibits ERK. MEK activates ERK.'
self.model = \
stmts_kstring_from_text(model_txt)
