def get_db_refs_by_name(ns, name, node_data):
"""Return standard name and grounding based on a namespace and a name.
Parameters
----------
ns : str
A name space in which the given name is interpreted.
name : str
The name in the given name space to get grounding for.
node_data : dict
Node data for logging purposes.
Returns
-------
name : str
The standardized name for the given entity.
db_refs : dict
The grounding for the given entity.
"""
db_refs = None
if ns == 'HGNC':
# Assumption: name is an HGNC symbol
hgnc_id = hgnc_client.get_current_hgnc_id(name)
if not hgnc_id:
logger.info("Invalid HGNC name: %s (%s)" % (name, node_data))
return name, None
elif isinstance(hgnc_id, list):
logger.info('More than one current HGNC ID for %s, choosing %s' %
(name, hgnc_id[0]))
hgnc_id = hgnc_id[0]
name = hgnc_client.get_hgnc_name(hgnc_id)
db_refs = {'HGNC': hgnc_id}
up_id = _get_up_id(hgnc_id)
if up_id:
db_refs['UP'] = up_id
mirbase_id = mirbase_client.get_mirbase_id_from_hgnc_id(hgnc_id)
if mirbase_id:
db_refs['MIRBASE'] = mirbase_id
elif ns in ('UNIPROT', 'UP'):
up_id = None
# This is a simple test to see if name is a valid UniProt ID,
# if we can't get a mnemonic, we assume it's not a UP ID
if uniprot_client.get_mnemonic(name, web_fallback=False):
up_id = name
# We next check if it's a mnemonic
else:
up_id_from_mnem = uniprot_client.get_id_from_mnemonic(name)
if up_id_from_mnem:
up_id = up_id_from_mnem
if not up_id:
logger.info('Couldn\'t get UP ID from %s' % name)
return name, None
db_refs = {'UP': up_id}
hgnc_id = uniprot_client.get_hgnc_id(up_id)
if hgnc_id:
db_refs['HGNC'] = hgnc_id
name = hgnc_client.get_hgnc_name(hgnc_id)
else:
name = uniprot_client.get_gene_name(up_id)
elif ns == 'FPLX':
db_refs = {'FPLX': name}
elif ns in ('GO', 'GOBP', 'GOCC'):
if name == 'cell proliferation':
name = 'cell population proliferation'
go_id = go_client.get_go_id_from_label(name)
if not go_id:
logger.info('Could not find GO ID for %s' % name)
return name, None
db_refs = {'GO': go_id}
name = go_client.get_go_label(go_id)
elif ns in ('MESHPP', 'MESHD', 'MESH'):
mesh_id, mesh_name = mesh_client.get_mesh_id_name(name)
if not mesh_id:
logger.info('Could not find MESH ID from %s' % name)
return name, None
name = mesh_name
db_refs = {'MESH': mesh_id}
# For now, handle MGI/RGD but putting the name into the db_refs so
# it's clear what namespace the name belongs to
# FIXME: Full implementation would look up MGI/RGD identifiers from
# the names, and obtain corresponding Uniprot IDs
elif ns == 'MGI':
up_id = mouse_lookup.get(name)
if up_id:
db_refs = {'UP': up_id}
elif ns == 'RGD':
up_id = rat_lookup.get(name)
if up_id:
db_refs = {'UP': up_id}
# Map Selventa families and complexes to FamPlex
elif ns == 'SFAM':
db_refs = {'SFAM': name}
indra_name = bel_to_indra.get(name)
if indra_name is None:
logger.info('Could not find mapping for BEL/SFAM family: '
'%s (%s)' % (name, node_data))
else:
db_refs['FPLX'] = indra_name
name = indra_name
elif ns == 'SCOMP':
db_refs = {'SCOMP': name}
indra_name = bel_to_indra.get(name)
if indra_name is None:
logger.info('Could not find mapping for BEL/SCOMP complex: '
'%s (%s)' % (name, node_data))
else:
db_refs['FPLX'] = indra_name
name = indra_name
# Map Entrez genes to HGNC/UP
elif ns in ('EGID', 'ENTREZ', 'NCBIGENE'):
hgnc_id = hgnc_client.get_hgnc_from_entrez(name)
db_refs = {'EGID': name}
if hgnc_id is not None:
db_refs['HGNC'] = hgnc_id
name = hgnc_client.get_hgnc_name(hgnc_id)
up_id = hgnc_client.get_uniprot_id(hgnc_id)
if up_id:
db_refs['UP'] = up_id
else:
logger.info(
'HGNC entity %s with HGNC ID %s has no '
'corresponding Uniprot ID.', name, hgnc_id)
mirbase_id = mirbase_client.get_mirbase_id_from_hgnc_id(hgnc_id)
if mirbase_id:
db_refs['MIRBASE'] = mirbase_id
else:
logger.debug('Could not map EGID%s to HGNC.' % name)
name = 'E%s' % name
elif ns == 'MIRBASE':
mirbase_id = mirbase_client.get_mirbase_id_from_mirbase_name(name)
if not mirbase_id:
logger.info('Could not map miRBase name %s to ID', name)
return name, None
db_refs = {'MIRBASE': mirbase_id}
hgnc_id = mirbase_client.get_hgnc_id_from_mirbase_id(mirbase_id)
if hgnc_id:
db_refs['HGNC'] = hgnc_id
name = hgnc_client.get_hgnc_name(hgnc_id)
# CHEBI
elif ns == 'CHEBI':
# We first look up BEL's own namespace map for ChEBI names to IDs
chebi_id = chebi_name_id.get(name)
# If that fails, we look up INDRA's ChEBI name to ID mapping
if not chebi_id:
chebi_id = chebi_client.get_chebi_id_from_name(name)
if chebi_id:
db_refs = {'CHEBI': chebi_id}
else:
logger.info('CHEBI name %s not found in map.' % name)
# These appear in the name slot but are actually IDs
elif ns == 'CHEBIID':
chebi_id = identifiers.ensure_chebi_prefix(name)
db_refs = {'CHEBI': chebi_id}
name = chebi_client.get_chebi_name_from_id(chebi_id)
# SDIS, SCHEM: Include the name as the ID for the namespace
elif ns in ('SDIS', 'SCHEM', 'TEXT'):
db_refs = {ns: name}
elif ns == 'TAX':
tid = taxonomy_client.get_taxonomy_id(name)
if tid:
db_refs = {'TAXONOMY': tid}
else:
logger.info('Could not get taxonomy ID for %s' % name)
else:
logger.info("Unhandled namespace: %s: %s (%s)" % (ns, name, node_data))
return name, db_refs
def refinement_of(self, other, ontology, entities_refined=False):
from indra.databases import go_client
# Make sure the Agent types match
if type(self) != type(other):
return False
# ENTITIES
# Check that the basic entity of the agent either matches or is related
# to the entity of the other agent. If not, no match.
# If the entities, match, then we can continue
if not (entities_refined or
(self.entity_matches(other) or self.isa(other, ontology))):
return False
# BOUND CONDITIONS
# Now check the bound conditions. For self to be a refinement of
# other in terms of the bound conditions, it has to include all of the
# bound conditions in the other agent, and add additional context.
# TODO: For now, we do not check the bound conditions of the bound
# conditions.
# FIXME: This matching procedure will get confused if the same
# entity is included more than once in one of the sets--this will
# be picked up as a match
# Iterate over the bound conditions in the other agent, and make sure
# they are all matched in self.
for bc_other in other.bound_conditions:
# Iterate over the bound conditions in self to find a match
bc_found = False
for bc_self in self.bound_conditions:
if (bc_self.is_bound == bc_other.is_bound) and \
bc_self.agent.refinement_of(bc_other.agent, ontology):
bc_found = True
# If we didn't find a match for this bound condition in self, then
# no refinement
if not bc_found:
return False
# MODIFICATIONS
# Similar to the above, we check that self has all of the modifications
# of other.
# Here we need to make sure that a mod in self.mods is only matched
# once to a mod in other.mods. Otherwise ('phoshporylation') would be
# considered a refinement of ('phosphorylation', 'phosphorylation')
matched_indices = []
# This outer loop checks that each modification in the other Agent
# is matched.
for other_mod in other.mods:
mod_found = False
# We need to keep track of indices for this Agent's modifications
# to make sure that each one is used at most once to match
# the modification of one of the other Agent's modifications.
for ix, self_mod in enumerate(self.mods):
if self_mod.refinement_of(other_mod, ontology):
# If this modification hasn't been used for matching yet
if ix not in matched_indices:
# Set the index as used
matched_indices.append(ix)
mod_found = True
break
# If we didn't find an exact match for this mod in other, then
# no refinement
if not mod_found:
return False
# MUTATIONS
# Similar to the above, we check that self has all of the mutations
# of other.
matched_indices = []
# This outer loop checks that each mutation in the other Agent
# is matched.
for other_mut in other.mutations:
mut_found = False
# We need to keep track of indices for this Agent's mutations
# to make sure that each one is used at most once to match
# the mutation of one of the other Agent's mutations.
for ix, self_mut in enumerate(self.mutations):
if self_mut.refinement_of(other_mut):
# If this mutation hasn't been used for matching yet
if ix not in matched_indices:
# Set the index as used
matched_indices.append(ix)
mut_found = True
break
# If we didn't find an exact match for this mut in other, then
# no refinement
if not mut_found:
return False
# LOCATION
# If the other location is specified and this one is not then self
# cannot be a refinement
if self.location is None:
if other.location is not None:
return False
# If both this location and the other one is specified, we check the
# hierarchy.
elif other.location is not None:
# If the other location is part of this location then
# self.location is not a refinement
sl = go_client.get_go_id_from_label(self.location)
ol = go_client.get_go_id_from_label(other.location)
if not ontology.isa_or_partof('GO', sl, 'GO', ol):
return False
# ACTIVITY
if self.activity is None:
if other.activity is not None:
return False
elif other.activity is not None:
if not self.activity.refinement_of(other.activity, ontology):
return False
# Everything checks out
return True
def get_db_refs_by_name(ns, name, node_data):
"""Return standard name and grounding based on a namespace and a name.
Parameters
----------
ns : str
A name space in which the given name is interpreted.
name : str
The name in the given name space to get grounding for.
node_data : dict
Node data for logging purposes.
Returns
-------
name : str
The standardized name for the given entity.
db_refs : dict
The grounding for the given entity.
"""
db_refs = None
if ns == 'HGNC':
hgnc_id = hgnc_client.get_hgnc_id(name)
if not hgnc_id:
logger.info("Invalid HGNC name: %s (%s)" % (name, node_data))
return name, None
db_refs = {'HGNC': hgnc_id}
up_id = _get_up_id(hgnc_id)
if up_id:
db_refs['UP'] = up_id
mirbase_id = mirbase_client.get_mirbase_id_from_hgnc_id(hgnc_id)
if mirbase_id:
db_refs['MIRBASE'] = mirbase_id
elif ns in ('UNIPROT', 'UP'):
up_id = None
gene_name = uniprot_client.get_gene_name(name)
if gene_name:
up_id = name
else:
up_id_from_mnem = uniprot_client.get_id_from_mnemonic(name)
if up_id_from_mnem:
up_id = up_id_from_mnem
gene_name = uniprot_client.get_gene_name(up_id)
if not up_id:
logger.info('Couldn\'t get UP ID from %s' % name)
return name, None
db_refs = {'UP': up_id}
if uniprot_client.is_human(up_id):
hgnc_id = hgnc_client.get_hgnc_id(gene_name)
if not hgnc_id:
logger.info('Uniprot ID linked to invalid human gene '
'name %s' % name)
else:
db_refs['HGNC'] = hgnc_id
elif ns == 'FPLX':
db_refs = {'FPLX': name}
elif ns in ('GO', 'GOBP', 'GOCC'):
go_id = go_client.get_go_id_from_label(name)
if not go_id:
logger.info('Could not find GO ID for %s' % name)
return name, None
db_refs = {'GO': go_id}
elif ns in ('MESHPP', 'MESHD', 'MESH'):
mesh_id = mesh_client.get_mesh_id_name(name)
if not mesh_id:
logger.info('Could not find MESH ID fro %s' % name)
return name, None
db_refs = {'MESH': mesh_id}
# For now, handle MGI/RGD but putting the name into the db_refs so
# it's clear what namespace the name belongs to
# FIXME: Full implementation would look up MGI/RGD identifiers from
# the names, and obtain corresponding Uniprot IDs
elif ns in ('MGI', 'RGD'):
db_refs = {ns: name}
# Map Selventa families to FamPlexes
elif ns == 'SFAM':
db_refs = {'SFAM': name}
indra_name = bel_to_indra.get(name)
if indra_name is None:
logger.info('Could not find mapping for BEL/SFAM family: '
'%s (%s)' % (name, node_data))
else:
db_refs['FPLX'] = indra_name
name = indra_name
# Map Entrez genes to HGNC/UP
elif ns in ('EGID', 'ENTREZ', 'NCBIGENE'):
hgnc_id = hgnc_client.get_hgnc_from_entrez(name)
db_refs = {'EGID': name}
if hgnc_id is not None:
db_refs['HGNC'] = hgnc_id
name = hgnc_client.get_hgnc_name(hgnc_id)
up_id = hgnc_client.get_uniprot_id(hgnc_id)
if up_id:
db_refs['UP'] = up_id
else:
logger.info('HGNC entity %s with HGNC ID %s has no '
'corresponding Uniprot ID.',
name, hgnc_id)
mirbase_id = mirbase_client.get_mirbase_id_from_hgnc_id(hgnc_id)
if mirbase_id:
db_refs['MIRBASE'] = mirbase_id
else:
logger.info('Could not map EGID%s to HGNC.' % name)
name = 'E%s' % name
elif ns == 'MIRBASE':
mirbase_id = mirbase_client.get_mirbase_id_from_mirbase_name(name)
if not mirbase_id:
logger.info('Could not map miRBase name %s to ID', name)
return
db_refs = {'MIRBASE': mirbase_id}
hgnc_id = mirbase_client.get_hgnc_id_from_mirbase_id(mirbase_id)
if hgnc_id:
db_refs['HGNC'] = hgnc_id
# CHEBI
elif ns == 'CHEBI':
chebi_id = chebi_name_id.get(name)
if not chebi_id:
chebi_id = chebi_client.get_chebi_id_from_name(name)
if chebi_id:
db_refs = {'CHEBI': chebi_id}
else:
logger.info('CHEBI name %s not found in map.' % name)
# SDIS, SCHEM: Include the name as the ID for the namespace
elif ns in ('SDIS', 'SCHEM'):
db_refs = {ns: name}
else:
logger.info("Unhandled namespace: %s: %s (%s)" % (ns, name,
node_data))
return name, db_refs
def test_go_label_to_id():
assert go_client.get_go_id_from_label('mitochondrion inheritance') == \
'GO:0000001'
def test_partof_comp_not():
assert not bio_ontology.isa_or_partof(
'GO', go_client.get_go_id_from_label('cellular_component'), 'GO',
go_client.get_go_id_from_label('cytoplasm'))