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_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_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