def get_members(agent):
dbname, dbid = agent.get_grounding()
if dbname not in ['FPLX', 'BE']:
return None
eh = hierarchies['entity']
uri = eh.get_uri(dbname, dbid)
children_uris = sorted(eh.get_children(uri))
children_agents = [
expand_families._agent_from_uri(uri) for uri in children_uris
]
return children_agents
def _get_members(agent):
if 'FPLX' not in agent.db_refs:
return None
dbname, dbid = 'FPLX', agent.db_refs['FPLX']
eh = hierarchies['entity']
uri = eh.get_uri(dbname, dbid)
children_uris = sorted(eh.get_children(uri))
children_agents = [
expand_families._agent_from_uri(uri) for uri in children_uris
]
return children_agents
def suggest_relevant_relations(groundings):
def make_nice_list(lst):
if len(lst) == 1:
return lst[0]
pre = ', '.join(lst[:-1])
full = '%s, or %s' % (pre, lst[-1])
return full
prefix1 = 'By the way, I recognized'
prefix2 = 'I also recognized'
msg_parts = []
for entity_txt, (dbn, dbi) in groundings.items():
if dbn == 'FPLX':
ag = Agent(name=entity_txt, db_refs={dbn: dbi})
children = expander.get_children(ag)
print(children)
if not children:
continue
children_names = [ch[1] for ch in children]
children_str = make_nice_list(children_names)
prefix = prefix1 if not msg_parts else prefix2
msg = ('%s "%s" as a family or complex, '
'you might be interested in asking about some of its '
'specific members like %s.') % (prefix, entity_txt,
children_str)
msg_parts.append(msg)
if dbn == 'HGNC':
name = hgnc_client.get_hgnc_name(dbi)
uri = expander.entities.get_uri(dbn, name)
print(uri)
parent_uris = expander.entities.get_parents(uri)
parents = [
expand_families._agent_from_uri(uri) for uri in parent_uris
]
print(parents)
if not parents:
continue
parent_names = [p.name for p in parents]
parents_str = make_nice_list(parent_names)
prefix = prefix1 if not msg_parts else prefix2
msg = ('%s "%s" as a protein that is part of a family or complex, '
'you might be interested in asking about some of those too '
'like %s.') % (prefix, entity_txt, parents_str)
msg_parts.append(msg)
full_msg = ' '.join(msg_parts)
return full_msg
def get_binding_site_name(agent):
"""Return a binding site name from a given agent."""
# Try to construct a binding site name based on parent
grounding = agent.get_grounding()
if grounding != (None, None):
uri = hierarchies['entity'].get_uri(grounding[0], grounding[1])
# Get highest level parents in hierarchy
parents = hierarchies['entity'].get_parents(uri, 'top')
if parents:
# Choose the first parent if there are more than one
parent_uri = sorted(parents)[0]
parent_agent = _agent_from_uri(parent_uri)
binding_site = _n(parent_agent.name).lower()
return binding_site
# Fall back to Agent's own name if one from parent can't be constructed
binding_site = _n(agent.name).lower()
return binding_site
def get_binding_site_name(agent):
"""Return a binding site name from a given agent."""
# Try to construct a binding site name based on parent
grounding = agent.get_grounding()
if grounding != (None, None):
uri = hierarchies['entity'].get_uri(grounding[0], grounding[1])
# Get highest level parents in hierarchy
parents = hierarchies['entity'].get_parents(uri, 'top')
if parents:
# Choose the first parent if there are more than one
parent_uri = sorted(parents)[0]
parent_agent = _agent_from_uri(parent_uri)
binding_site = _n(parent_agent.name).lower()
return binding_site
# Fall back to Agent's own name if one from parent can't be constructed
binding_site = _n(agent.name).lower()
return binding_site