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