def enrich_drug_inchi(self, graph: BELGraph) -> None:
"""Enrich drugs in the graph with their InChI equivalent nodes."""
self.add_namespace_to_graph(graph)
for node, drug_model in list(self.iter_drugs(graph)):
if drug_model.inchi:
graph.add_equivalence(node, drug_model.as_inchi_bel())
def append_equivalences_graph(df: pd.DataFrame, graph: BELGraph) -> None:
"""Append equivalence relations to the graph."""
graph.namespace_url.update(famplex_to_belns)
graph.namespace_pattern.update({
identifiers_key: pattern
for _, (identifiers_key, pattern) in famplex_to_identifiers.items()
})
for index, (namespace, name, famplex_name) in df.iterrows():
is_complex = "complex" in name.lower()
if is_complex:
func = named_complex_abundance
else:
func = protein
if namespace in famplex_to_belns:
if is_complex:
namespace = "SCOMP"
else:
namespace = "SFAM"
elif namespace in famplex_to_identifiers:
namespace = famplex_to_identifiers[namespace][0]
else:
continue
external = func(namespace, name)
famplex = func('FPLX', famplex_name)
graph.add_equivalence(external, famplex)
def test_indirect_has_namespace(self):
graph = BELGraph()
a = Protein(namespace='HGNC', name='CD33')
b = Protein(namespace='HGNCID', identifier='1659')
graph.add_equivalence(a, b)
self.assertEqual({a, b}, graph.get_equivalent_nodes(a))
self.assertEqual({a, b}, graph.get_equivalent_nodes(b))
self.assertTrue(graph.node_has_namespace(a, 'HGNC'))
self.assertTrue(graph.node_has_namespace(b, 'HGNC'))
def to_bel(self) -> BELGraph:
"""Convert miRBase to BEL."""
result = BELGraph()
for sequence in self._get_query(Sequence):
mirbase_node = sequence.as_pybel()
for xref in sequence.xrefs:
result.add_equivalence(
mirbase_node,
MicroRna(
namespace=xref.database,
identifier=xref.database_id,
))
return result
def test_triangle_has_namespace(self):
graph = BELGraph()
a = Protein(namespace='A', name='CD33')
b = Protein(namespace='B', identifier='1659')
c = Protein(namespace='C', identifier='1659')
d = Protein(namespace='HGNC', identifier='1659')
graph.add_equivalence(a, b)
graph.add_equivalence(b, c)
graph.add_equivalence(c, a)
graph.add_equivalence(c, d)
self.assertEqual({a, b, c, d}, graph.get_equivalent_nodes(a))
self.assertEqual({a, b, c, d}, graph.get_equivalent_nodes(b))
self.assertEqual({a, b, c, d}, graph.get_equivalent_nodes(c))
self.assertEqual({a, b, c, d}, graph.get_equivalent_nodes(d))
self.assertTrue(graph.node_has_namespace(a, 'HGNC'))
self.assertTrue(graph.node_has_namespace(b, 'HGNC'))
self.assertTrue(graph.node_has_namespace(c, 'HGNC'))
self.assertTrue(graph.node_has_namespace(d, 'HGNC'))
def enrich_drug_equivalences(self, graph: BELGraph) -> None:
"""Enrich drugs in the graph with their equivalent nodes."""
self.add_namespace_to_graph(graph)
for node, drug_model in list(self.iter_drugs(graph)):
if drug_model.inchi:
graph.add_equivalence(node, drug_model.as_inchi_bel())
if drug_model.inchikey:
graph.add_equivalence(node, drug_model.as_inchikey_bel())
for xref in drug_model.xrefs:
resource = xref.resource.lower()
identifier = xref.identifier
if xref.resource in {'chebi', 'chembl'}:
graph.add_equivalence(
node,
abundance(namespace=resource, identifier=identifier))
elif xref.resource == 'KEGG Compound':
# https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000013
graph.add_equivalence(
node,
abundance(namespace='kegg.compound',
identifier=identifier))
elif xref.resource == 'PubChem Substance':
# https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000033
graph.add_equivalence(
node,
abundance(namespace='pubchem.substance',
identifier=identifier))
elif xref.resource == 'PubChem Compound':
# https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000034
graph.add_equivalence(
node,
abundance(namespace='pubchem.compound',
identifier=identifier))
def enrich_equivalences(self, graph: BELGraph) -> None:
"""Add equivalent node information."""
self.add_namespace_to_graph(graph)
for node, gene_model in list(self.iter_genes(graph)):
graph.add_equivalence(node, gene_model.as_bel(node[FUNCTION]))