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 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_mirbase_name_to_id():
assert 'MI0000075' == \
mirbase_client.get_mirbase_id_from_mirbase_name('hsa-mir-19b-2')
def get_agent(node_data, node_modifier_data=None):
# FIXME: Handle translocations on the agent for ActiveForms, turn into
# location conditions
# Check the node type/function
node_func = node_data[pc.FUNCTION]
if node_func not in (pc.PROTEIN, pc.RNA, pc.BIOPROCESS, pc.COMPLEX,
pc.PATHOLOGY, pc.ABUNDANCE, pc.MIRNA):
mod_data = node_modifier_data or 'No node data'
logger.info("Nodes of type %s not handled: %s", node_func, mod_data)
return None
# Skip gene/protein fusions
if pc.FUSION in node_data:
logger.info("Gene and protein fusions not handled: %s" %
str(node_data))
return None
# COMPLEXES ------------
# First, handle complexes, which will consist recursively of other agents
if node_func == pc.COMPLEX:
# First, check for members: if there are no members, we assume this
# is a named complex
members = node_data.get(pc.MEMBERS)
if members is None:
return None
# Otherwise, get the "main" agent, to which the other members will be
# attached as bound conditions
main_agent = get_agent(members[0])
# If we can't get the main agent, return None
if main_agent is None:
return None
bound_conditions = [
BoundCondition(get_agent(m), True) for m in members[1:]
]
# Check the bound_conditions for any None agents
if any([bc.agent is None for bc in bound_conditions]):
return None
main_agent.bound_conditions = bound_conditions
# Get activity of main agent
ac = _get_activity_condition(node_modifier_data)
main_agent.activity = ac
return main_agent
# OTHER NODE TYPES -----
# Get node identifier information
name = node_data.get(pc.NAME)
ns = node_data[pc.NAMESPACE]
ident = node_data.get(pc.IDENTIFIER)
# No ID present, get identifier using the name, namespace
db_refs = None
if not ident:
assert name, "Node must have a name if lacking an identifier."
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 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
# FIXME: Look up go ID in ontology lookup service
# FIXME: Look up MESH IDs from name
# FIXME: For now, just use node name
elif ns in ('GOBP', 'MESHPP', 'MESHD'):
db_refs = {}
# 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 == 'EGID':
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 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:
print("Unhandled namespace: %s: %s (%s)" % (ns, name, node_data))
# We've already got an identifier, look up other identifiers if necessary
else:
# Get the name, overwriting existing name if necessary
if ns == 'HGNC':
name = hgnc_client.get_hgnc_name(ident)
db_refs = {'HGNC': ident}
up_id = _get_up_id(ident)
if up_id:
db_refs['UP'] = up_id
mirbase_id = mirbase_client.get_mirbase_id_from_hgnc_id(ident)
if mirbase_id:
db_refs['MIRBASE'] = mirbase_id
elif ns == 'UP':
db_refs = {'UP': ident}
name = uniprot_client.get_gene_name(ident)
assert name
if uniprot_client.is_human(ident):
hgnc_id = hgnc_client.get_hgnc_id(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 == 'MIRBASE':
db_refs = {'MIRBASE': ident}
elif ns in ('MGI', 'RGD'):
raise ValueError('Identifiers for MGI and RGD databases are not '
'currently handled: %s' % node_data)
else:
print("Unhandled namespace with identifier: %s: %s (%s)" %
(ns, name, node_data))
if db_refs is None:
logger.info('Unable to get identifier information for node: %s',
node_data)
return None
# Get modification conditions
mods, muts = _get_all_pmods(node_data)
# Get activity condition
ac = _get_activity_condition(node_modifier_data)
to_loc = _get_translocation_target(node_modifier_data)
# Check for unhandled node modifiers, skip if so
if _has_unhandled_modifiers(node_modifier_data):
return None
# Make the agent
ag = Agent(name,
db_refs=db_refs,
mods=mods,
mutations=muts,
activity=ac,
location=to_loc)
return ag