def get_chemical_agent(name, mesh_id, cas_id):
db_refs = {'MESH': mesh_id}
if cas_id:
db_refs['CAS'] = cas_id
db_refs = standardize_db_refs(db_refs)
assert_valid_db_refs(db_refs)
return Agent(name, db_refs=db_refs)
def get_standard_agent(name, db_refs, ontology=None, ns_order=None, **kwargs):
"""Get a standard agent based on the name, db_refs, and a any other kwargs.
name : str
The name of the agent that may not be standardized.
db_refs : dict
A dict of db refs that may not be standardized, i.e., may be
missing an available UP ID corresponding to an existing HGNC ID.
ontology : Optional[indra.ontology.IndraOntology]
An IndraOntology object, if not provided, the default BioOntology
is used.
ns_order : Optional[list]
A list of namespaces which are in order of priority with higher
priority namespaces appearing earlier in the list.
kwargs :
Keyword arguments to pass to :func:`Agent.__init__`.
Returns
-------
Agent
A standard agent
"""
standard_name, db_refs = standardize_name_db_refs(db_refs,
ontology=ontology,
ns_order=ns_order)
if standard_name:
name = standard_name
assert_valid_db_refs(db_refs)
return Agent(name, db_refs=db_refs, **kwargs)
def _get_drug_agent(drug_element):
name_tag = db_find(drug_element, 'db:name')
name = name_tag.text
db_refs = {}
# Extract the DrugBank ID
drugbank_id_tags = db_findall(drug_element, 'db:drugbank-id')
# We do a sort here because sometimes there's more than one
# DrugBank ID and we choose the "smaller" one here
drugbank_id = sorted([di.text for di in drugbank_id_tags
if di.text.startswith('DB')])[0]
db_refs['DRUGBANK'] = drugbank_id
# Extract CAS ID
cas_tag = db_find(drug_element, 'db:cas-number')
if cas_tag is not None and cas_tag.text is not None:
db_refs['CAS'] = cas_tag.text
# Extract other xrefs
for xref_tag in db_findall(drug_element, 'db:external-identifiers/'
'db:external-identifier'):
resource = db_find(xref_tag, 'db:resource').text
identifier = db_find(xref_tag, 'db:identifier').text
if resource == 'ChEMBL':
db_refs['CHEMBL'] = ensure_chembl_prefix(identifier)
elif resource == 'PubChem Compound':
db_refs['PUBCHEM'] = identifier
elif resource == 'ChEBI':
db_refs['CHEBI'] = ensure_chebi_prefix(identifier)
assert_valid_db_refs(db_refs)
return get_standard_agent(name, db_refs)
def assert_valid_node(self, label):
db_ns, db_id = self.get_ns_id(label)
if db_ns in {'INDRA_ACTIVITIES', 'INDRA_MODS'}:
return
try:
assert_valid_db_refs({db_ns: db_id})
except Exception as e:
logger.warning(e)
def get_context(organism_name, organism_tax_id):
if not organism_tax_id:
return None
tax_id = str(int(organism_tax_id))
db_refs = {'TAXONOMY': tax_id}
assert_valid_db_refs(db_refs)
species = RefContext(organism_name, db_refs=db_refs)
bc = BioContext(species=species)
return bc
def _extract_protein(self, name, gene_id):
refs = {'EGID': gene_id}
hgnc_id = hgnc_client.get_hgnc_from_entrez(gene_id)
if hgnc_id is not None:
refs['HGNC'] = hgnc_id
standard_name, db_refs = standardize_name_db_refs(refs)
if standard_name:
name = standard_name
assert_valid_db_refs(db_refs)
return Agent(name, db_refs=db_refs)
def get_gene_agent(name, gene_entrez_id):
db_refs = {'EGID': gene_entrez_id}
hgnc_id = hgnc_client.get_hgnc_id(name)
if hgnc_id:
db_refs['HGNC'] = hgnc_id
standard_name, db_refs = standardize_name_db_refs(db_refs)
assert_valid_db_refs(db_refs)
if standard_name:
name = standard_name
return Agent(name, db_refs=db_refs)
def get_disease_agent(name, disease_id):
groundings = disease_id.split('|')
db_refs = {}
for gr in groundings:
db_ns, db_id = gr.split(':')
db_refs[db_ns] = db_id
standard_name, db_refs = standardize_name_db_refs(db_refs)
assert_valid_db_refs(db_refs)
if standard_name:
name = standard_name
return Agent(name, db_refs=db_refs)
def process_selventa_xref(xref):
if pandas.isna(xref):
return ''
db_refs = {}
for xref_part in xref.split('|'):
prefix, db_id = xref_part.split(':', maxsplit=1)
ns = xref_mappings.get(prefix)
if not ns:
logger.info('Unknown namespace: %s' % prefix)
continue
db_id = ensure_prefix_if_needed(ns, db_id)
db_refs[ns] = db_id
assert_valid_db_refs(db_refs)
db_refs_str = '|'.join(['%s:%s' % (k, v)
for k, v in sorted(db_refs.items())])
return db_refs_str
def _extract_drugs(self, compound_ids, lspci_id):
drugs = []
for id_ in compound_ids.split('|'):
db_refs = {'LSPCI': lspci_id}
if id_.startswith('CHEMBL'):
db_refs['CHEMBL'] = id_
elif id_.startswith('HMSL'):
db_refs['HMS-LINCS'] = id_.split('HMSL')[1]
else:
logger.warning('Unhandled ID type: %s' % id_)
# Name standardization finds correct names but because
# ChEMBL is incomplete as a local resource, we don't
# universally standardize its names, instead, we look
# it up explicitly when necessary.
name, db_refs = standardize_name_db_refs(db_refs)
if name is None:
# This is one way to detect that the drug could not be
# standardized beyond just its name so in the
# standardized_only condition, we skip this drug
if self.standardized_only:
continue
elif 'HMS-LINCS' in db_refs:
name = \
lincs_client_obj.get_small_molecule_name(
db_refs['HMS-LINCS'])
elif 'CHEMBL' in db_refs:
name = chembl_client.get_chembl_name(db_refs['CHEMBL'])
# If name is still None, we just use the ID as the name
if name is None:
# With the named_only restriction, we skip drugs without
# a proper name.
if self.named_only:
continue
name = id_
assert_valid_db_refs(db_refs)
drugs.append(Agent(name, db_refs=db_refs))
drugs = list({agent.matches_key():
agent for agent in drugs}.values())
return drugs