def test_read_nt3():
"""
Read from an RDF N-Triple file using RdfSource, with user defined
node property predicates.
"""
node_property_predicates = {
f"https://www.example.org/UNKNOWN/{x}"
for x in ["fusion", "homology", "combined_score", "cooccurence"]
}
t = Transformer()
source = RdfSource(t)
source.set_node_property_predicates(node_property_predicates)
g = source.parse(filename=os.path.join(RESOURCE_DIR, "rdf", "test2.nt"),
format="nt")
nodes, edges = load_graph_dictionary(g)
assert len(nodes) == 4
assert len(edges) == 3
n1 = nodes["ENSEMBL:ENSG0000000000001"]
assert n1["type"] == "SO:0000704"
assert len(n1["category"]) == 4
assert "biolink:Gene" in n1["category"]
assert "biolink:GenomicEntity" in n1["category"]
assert "biolink:NamedThing" in n1["category"]
assert n1["name"] == "Test Gene 123"
assert n1["description"] == "This is a Test Gene 123"
assert "Test Dataset" in n1["provided_by"]
n2 = nodes["ENSEMBL:ENSG0000000000002"]
assert n2["type"] == "SO:0000704"
assert len(n2["category"]) == 4
assert "biolink:Gene" in n2["category"]
assert "biolink:GenomicEntity" in n2["category"]
assert "biolink:NamedThing" in n1["category"]
assert n2["name"] == "Test Gene 456"
assert n2["description"] == "This is a Test Gene 456"
assert "Test Dataset" in n2["provided_by"]
e1 = edges["ENSEMBL:ENSP0000000000001", "ENSEMBL:ENSP0000000000002"][0]
assert e1["subject"] == "ENSEMBL:ENSP0000000000001"
assert e1["object"] == "ENSEMBL:ENSP0000000000002"
assert e1["predicate"] == "biolink:interacts_with"
assert e1["relation"] == "biolink:interacts_with"
assert e1["type"] == "biolink:Association"
assert e1["id"] == "urn:uuid:fcf76807-f909-4ccb-b40a-3b79b49aa518"
assert e1["fusion"] == "0"
assert e1["homology"] == "0.0"
assert e1["combined_score"] == "490.0"
assert e1["cooccurence"] == "332"
def test_read_nt6():
prefix_map = {
"HGNC":
"https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",
"OMIM": "http://omim.org/entry/",
}
node_property_predicates = {
"http://purl.obolibrary.org/obo/RO_0002558",
"http://purl.org/dc/elements/1.1/source",
"https://monarchinitiative.org/frequencyOfPhenotype",
}
predicate_mapping = {
"https://monarchinitiative.org/frequencyOfPhenotype":
"frequency_of_phenotype"
}
filename = os.path.join(RESOURCE_DIR, "rdf", "oban-test.nt")
t = Transformer()
source = RdfSource(t)
source.set_prefix_map(prefix_map)
source.set_node_property_predicates(node_property_predicates)
source.set_predicate_mapping(predicate_mapping)
g = source.parse(filename=filename, format="nt")
nodes, edges = load_graph_dictionary(g)
assert len(nodes.keys()) == 14
assert len(edges.keys()) == 7
n1 = nodes["HP:0000505"]
assert len(n1["category"]) == 1
assert "biolink:NamedThing" in n1["category"]
e1 = edges["OMIM:166400", "HP:0000006"][0]
assert e1["subject"] == "OMIM:166400"
assert e1["object"] == "HP:0000006"
assert e1["relation"] == "RO:0000091"
assert e1["type"] == "OBAN:association"
assert e1["has_evidence"] == "ECO:0000501"
e2 = edges["ORPHA:93262", "HP:0000505"][0]
assert e2["subject"] == "ORPHA:93262"
assert e2["object"] == "HP:0000505"
assert e2["relation"] == "RO:0002200"
assert e2["type"] == "OBAN:association"
assert e2["frequency_of_phenotype"] == "HP:0040283"
def test_read_nt2():
"""
Read from an RDF N-Triple file using RdfSource.
This test also supplies the knowledge_source parameter.
"""
t = Transformer()
s = RdfSource(t)
g = s.parse(
os.path.join(RESOURCE_DIR, "rdf", "test1.nt"),
provided_by="Test Dataset",
knowledge_source="Test Dataset",
)
nodes, edges = load_graph_dictionary(g)
assert len(nodes) == 2
assert len(edges) == 1
n1 = nodes["ENSEMBL:ENSG0000000000001"]
assert n1["type"] == "SO:0000704"
assert len(n1["category"]) == 4
assert "biolink:Gene" in n1["category"]
assert "biolink:GenomicEntity" in n1["category"]
assert "biolink:NamedThing" in n1["category"]
assert n1["name"] == "Test Gene 123"
assert n1["description"] == "This is a Test Gene 123"
assert "Test Dataset" in n1["provided_by"]
n2 = nodes["ENSEMBL:ENSG0000000000002"]
assert n2["type"] == "SO:0000704"
assert len(n2["category"]) == 4
assert "biolink:Gene" in n2["category"]
assert "biolink:GenomicEntity" in n2["category"]
assert "biolink:NamedThing" in n1["category"]
assert n2["name"] == "Test Gene 456"
assert n2["description"] == "This is a Test Gene 456"
assert "Test Dataset" in n2["provided_by"]
e = list(edges.values())[0][0]
assert e["subject"] == "ENSEMBL:ENSG0000000000001"
assert e["object"] == "ENSEMBL:ENSG0000000000002"
assert e["predicate"] == "biolink:interacts_with"
assert e["relation"] == "biolink:interacts_with"
assert "Test Dataset" in e["knowledge_source"]