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