def get_agent_from_grounding(grounding, up_web_fallback=False):
"""Return an INDRA Agent based on a grounding annotation."""
db_ns, db_id = grounding.split(':')
# Assume UniProt or RefSeq IDs
assert db_ns in {'uniprotkb', 'refseq', 'ddbj/embl/genbank'}, db_ns
if db_ns == 'uniprotkb':
if '-' in db_id:
up_id, feat_id = db_id.split('-')
# Assume it's a feature ID
assert feat_id.startswith('PRO'), feat_id
db_refs = {'UP': up_id, 'UPPRO': feat_id}
else:
db_refs = {'UP': db_id}
elif db_ns == 'refseq':
db_refs = {'REFSEQ_PROT': db_id}
else:
db_refs = {'GENBANK': db_id}
agent = Agent(db_id, db_refs=db_refs)
standardized = standardize_agent_name(agent)
if up_web_fallback:
# Handle special case of unreviewed UP entries
if not standardized and 'UP' in db_refs:
name = uniprot_client.get_gene_name(db_refs['UP'],
web_fallback=True)
if name:
agent.name = name
return agent
def get_virus_agent(name):
db_ns, db_id = virus_grounding_map[name].split(':')
db_refs = {db_ns: db_id}
ag = Agent(name, db_refs=db_refs)
mapped_label = virus_label_map.get('%s:%s' % (db_ns, db_id))
if mapped_label:
ag.name = mapped_label
else:
standardize_agent_name(ag, standardize_refs=True)
return ag
