def create_message(self):
target = ekb_kstring_from_text(self.target)
drug = ekb_kstring_from_text(self.drug)
content = KQMLList('IS-DRUG-TARGET')
content.set('target', target)
content.set('drug', drug)
return get_request(content), content
def create_message(self):
content = KQMLList('GET-COMMON')
ekb = ekb_from_text('MEK')
content.sets('genes', ekb)
content.sets('up-down', 'ONT::SUCCESSOR')
msg = get_request(content)
return msg, content
def create_message(self):
content = KQMLList('PHOSPHORYLATION-ACTIVATING')
content.sets('target', ekb_from_text('MAPK1'))
for name, value in [('residue', 'T'), ('position', '185')]:
if value is not None:
content.sets(name, value)
msg = get_request(content)
return msg, content
def create_message(self):
content = KQMLList('GET-PAPER-MODEL')
content.set('pmid', 'PMID-27906130')
return get_request(content), content
def create_message(self):
content = KQMLList('MODEL-UNDO')
msg = get_request(content)
return msg, content
def create_statements(self):
content = KQMLList('INDRA-TO-NL')
content.sets('statements', json.dumps(stmts_to_json(self.statements)))
return get_request(content), content
def create_message(self):
content = _get_qca_content('FIND-QCA-PATH', 'SOS1', 'KRAS')
msg = get_request(content)
return msg, content
def create_message(self):
content = KQMLList('FIND-COMMON-UPSTREAMS')
genes = ekb_from_text('AKT1, BRAF and MAPK1')
content.sets('genes', str(genes))
msg = get_request(content)
return msg, content
def create_message(self):
disease = ekb_kstring_from_text('common cold')
content = KQMLList('FIND-TREATMENT')
content.set('disease', disease)
return get_request(content), content
def create_message(self):
drug = agent_clj_from_text('SB525334')
content = KQMLList('FIND-DRUG-TARGETS')
content.set('drug', drug)
return get_request(content), content
def create_message(self):
disease = agent_clj_from_text('common cold')
content = KQMLList('FIND-TREATMENT')
content.set('disease', disease)
return get_request(content), content
def _get_expand_model_request(text, model_id):
content = KQMLList('EXPAND-MODEL')
descr = stmts_clj_from_text(text)
content.set('description', descr)
content.set('model-id', model_id)
return get_request(content), content
def create_message_04_reset(self):
time.sleep(2)
content = KQMLList('RESET-CAUSALITY-INDICES')
msg = get_request(content)
return msg, content
def create_message(self):
content = _get_qca_content('FIND-QCA-PATH', 'MAP2K1', 'BRAF')
msg = get_request(content)
return msg, content
def create_message(self):
content = _get_qca_content('FIND-QCA-PATH', 'SOS1', 'KRAS')
msg = get_request(content)
return msg, content
def create_message_4(self):
content = KQMLList('FIND-CELLULAR-LOCATION-FROM-NAMES')
content.set('genes', ['MAPK1', 'RAS'])
msg = get_request(content)
return msg, content
def create_message_failure(self):
content = KQMLList('FIND-MUTEX')
gene = ekb_from_text('BRAF')
content.set('gene', gene)
msg = get_request(content)
return msg, content
def create_message_failure(self):
content = KQMLList('FIND-COMMON-UPSTREAMS')
genes = ekb_from_text('UGT2B10, PTEN')
content.sets('genes', str(genes))
msg = get_request(content)
return msg, content
def create_message(self):
target = agent_clj_from_text(self.target)
content = KQMLList('FIND-TARGET-DRUG')
content.set('target', target)
return get_request(content), content
def create_message(self):
content = KQMLList('DESCRIBE-MODEL')
content.set('model-id', '1')
msg = get_request(content)
return msg, content
def create_message(self):
disease = agent_clj_from_text('prostate cancer')
content = KQMLList('FIND-DISEASE-TARGETS')
content.set('disease', disease)
return get_request(content), content
def create_message(self):
content = KQMLList('DESCRIBE-MODEL')
content.set('model-id', str(self.bioagent.mra.id_counter))
msg = get_request(content)
return msg, content
def create_message(self):
drug = ekb_kstring_from_text('SB525334')
content = KQMLList('FIND-DRUG-TARGETS')
content.set('drug', drug)
return get_request(content), content
def create_message(self):
content = KQMLList('BUILD-MODEL')
content.sets('description', '')
content.sets('format', 'ekb')
msg = get_request(content)
return msg, content
def create_message(self):
disease = ekb_kstring_from_text('lung cancer')
content = KQMLList('FIND-DISEASE-TARGETS')
content.set('disease', disease)
return get_request(content), content
def create_get_json(self):
content = KQMLList('MODEL-GET-JSON')
content.sets('model-id', '1')
msg = get_request(content)
return msg, content
def create_message(self):
target = ekb_kstring_from_text(self.target)
content = KQMLList('FIND-TARGET-DRUG')
content.set('target', target)
return get_request(content), content
def create_get_json(self):
content = KQMLList('MODEL-GET-JSON')
msg = get_request(content)
return msg, content
def create_message(self):
content = _get_qca_content('FIND-QCA-PATH', 'MAP2K1', 'BRAF')
msg = get_request(content)
return msg, content
def create_remove2(self):
content = KQMLList('MODEL-REMOVE-MECHANISM')
content.set('model-id', '3')
content.set('description', stmts_clj_from_text('NRAS activates BRAF'))
msg = get_request(content)
return msg, content
def create_message(self):
content = _get_qca_content('FIND-QCA-PATH', *self.agents)
return get_request(content), content
def create_undo(self):
content = KQMLList('MODEL-UNDO')
content.sets('model-id', '4')
msg = get_request(content)
return msg, content
def create_remove(self):
content = KQMLList('MODEL-REMOVE-MECHANISM')
content.set('model-id', '1')
content.set('description', stmts_clj_from_text('Unphosphorylated ERK'))
msg = get_request(content)
return msg, content
def create_hasmech2(self):
content = KQMLList('MODEL-HAS-MECHANISM')
content.set('model-id', '1')
content.sets('description', stmts_clj_from_text('NRAS activates BRAF'))
msg = get_request(content)
return msg, content
def _get_content(self, task, **contents):
content = KQMLList(task)
for key, value in contents.items():
content.set(key, value)
msg = get_request(content)
return msg, content
def create_message_01_explainable(self):
source = ekb_kstring_from_text('AKT1')
content = KQMLList('DATASET-CORRELATED-ENTITY')
content.set('source', source)
msg = get_request(content)
return msg, content
