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): 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): 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): # Here we create a KQML request that the TFTA needs to respond to gene = ekb_kstring_from_text(self.gene) pathway = ekb_kstring_from_text(self.pathway) content = KQMLList('IS-PATHWAY-GENE') content.set('gene', gene) content.set('pathway', pathway) return get_request(content), content
def create_message(self): # Here we create a KQML request that the TFTA needs to respond to target = ekb_kstring_from_text(self.target) mirna = ekb_kstring_from_text(self.mirna) content = KQMLList('IS-MIRNA-TARGET') content.set('target', target) content.set('miRNA', mirna) return get_request(content), content
def create_message(self): # Here we create a KQML request that the TFTA needs to respond to tf = ekb_kstring_from_text(self.tf) target = ekb_kstring_from_text(self.target) content = KQMLList('IS-TF-TARGET') content.set('tf', tf) content.set('target', target) return get_request(content), content
def create_message2(self): condition_entity = ekb_kstring_from_text('Vemurafenib') target_entity = ekb_kstring_from_text('Inactive ERK') content = KQMLList('MODEL-COMPARE-CONDITIONS') content.set('model', self.model) content.set('agent', condition_entity) content.set('affected', target_entity) msg = get_request(content) return msg, content
def create_message_failure_3(self): source = ekb_kstring_from_text('RAS') target = ekb_kstring_from_text('MAPK1') content = KQMLList('FIND-CAUSAL-PATH') content.set('source', source) content.set('target', target) content.sets('direction', 'strict') msg = get_request(content) return msg, content
def create_message(self): # Here we create a KQML request that the TFTA needs to respond to tf = ekb_kstring_from_text(self.tf) print('tf=' + str(tf)) target = ekb_kstring_from_text(self.target) print('target=' + str(target)) tissue = self.tissue content = KQMLList('IS-TF-TARGET-TISSUE') content.set('tf', tf) content.set('target', target) content.set('tissue', tissue) print('content=' + str(content)) print('get_request(content)=' + str(get_request(content))) return get_request(content), content
def create_message_failure(self): time.sleep(2) source = ekb_kstring_from_text('ABC') content = KQMLList('DATASET-CORRELATED-ENTITY') content.set('source', source) msg = get_request(content) return msg, content
def create_message_failure_2(self): target = ekb_kstring_from_text('ABC') content = KQMLList('FIND-CAUSALITY-SOURCE') content.set('target', target) content.sets('type', 'phosphorylates') msg = get_request(content) return msg, content
def create_message_failure(self): source = ekb_kstring_from_text('MAPK1') content = KQMLList('FIND-CAUSALITY-TARGET') content.set('source', source) content.sets('type', 'activation') msg = get_request(content) return msg, content
def create_message_05_explainable_again(self): time.sleep(2) source = ekb_kstring_from_text('AKT1') content = KQMLList('DATASET-CORRELATED-ENTITY') content.set('source', source) msg = get_request(content) return msg, content
def create_message(self): # Here we create a KQML request that the TFTA needs to respond to gene = ekb_kstring_from_text(self.gene) keyword = self.keyword content = KQMLList('FIND-COMMON-PATHWAY-GENES-KEYWORD') content.set('gene', gene) content.set('keyword', keyword) return get_request(content), content
def create_message(self): # Here we create a KQML request that the TFTA needs to respond to target = ekb_kstring_from_text(self.target) tissue = self.tissue content = KQMLList('FIND-TARGET-TF-TISSUE') content.set('target', target) content.set('tissue', tissue) return get_request(content), content
def create_message(self): # Here we create a KQML request that the TFTA needs to respond to gene = ekb_kstring_from_text(self.gene) db = self.database content = KQMLList('FIND-PATHWAY-DB-GENE') content.set('gene', gene) content.set('database', db) return get_request(content), content
def create_message_PAAD(self): content = KQMLList('FIND-MUTATION-SIGNIFICANCE') gene = ekb_kstring_from_text('ACTN4') disease = ekb_from_text('pancreatic adenocarcinoma') content.set('gene', gene) content.set('disease', disease) msg = get_request(content) return msg, content
def create_message_failure_2(self): content = KQMLList('FIND-MUTATION-SIGNIFICANCE') gene = ekb_kstring_from_text('ABC') disease = ekb_from_text('breast cancer') content.set('gene', gene) content.set('disease', disease) msg = get_request(content) return msg, content
def _get_qca_content(task, source, target): """Get the KQMLList content to be sent to the QCA for given task. Paramters --------- source, target : str The strings representing the proteins for source and target, respectively, for example 'BRAF'. Returns ------- content : KQMLList The KQML content to be sent to the QCA module as part of the request. """ content = KQMLList(task) content.set('source', ekb_kstring_from_text(source)) content.set('target', ekb_kstring_from_text(target)) return content
def create_message_OV(self): content = KQMLList('FIND-MUTATION-FREQUENCY') gene = ekb_kstring_from_text('TP53') disease = ekb_from_text('Ovarian serous cystadenocarcinoma') content.set('gene', gene) content.set('disease', disease) msg = get_request(content) return msg, content
def _get_qca_content(task, source, target): """Get the KQMLList content to be sent to the QCA for given task. Paramters --------- source, target : str The strings representing the proteins for source and target, respectively, for example 'BRAF'. Returns ------- content : KQMLList The KQML content to be sent to the QCA module as part of the request. """ content = KQMLList(task) content.set('source', ekb_kstring_from_text(source)) content.set('target', ekb_kstring_from_text(target)) return content
def _get_build_model_request(text, format=None): content = KQMLList('BUILD-MODEL') if format == 'ekb': descr = ekb_kstring_from_text(text) content.sets('description', descr) content.sets('format', 'ekb') else: descr = stmts_clj_from_text(text) content.set('description', descr) return get_request(content), 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 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_message(self): # Here we create a KQML request that the TFTA needs to respond to mirna = ekb_kstring_from_text(self.mirna) content = KQMLList('FIND-GENE-COUNT-MIRNA') content.set('miRNA', mirna) return get_request(content), content
def create_message(self): # Here we create a KQML request that the TFTA needs to respond to target = ekb_kstring_from_text(self.target) content = KQMLList('FIND-MIRNA-COUNT-GENE') content.set('target', target) return get_request(content), 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): disease = ekb_kstring_from_text('common cold') content = KQMLList('FIND-TREATMENT') content.set('disease', disease) return get_request(content), content
def create_message(self): # Here we create a KQML request that the TFTA needs to respond to pathway = ekb_kstring_from_text(self.pathway) content = KQMLList('FIND-TF-PATHWAY') content.set('pathway', pathway) return get_request(content), 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 _get_expand_model_request(text, model_id): content = KQMLList('EXPAND-MODEL') descr = ekb_kstring_from_text(text) content.set('description', descr) content.set('model-id', model_id) return get_request(content), content
def _get_build_model_request(text): content = KQMLList('BUILD-MODEL') descr = ekb_kstring_from_text(text) content.set('description', descr) return get_request(content), content