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)