def test_read_nt5():
"""
Parse an OBAN styled NT, with user defined prefix_map and node_property_predicates.
"""
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",
}
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)
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["frequencyOfPhenotype"] == "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"]
def test_read_nt5():
"""
Parse an OBAN styled NT, with user defined prefix_map and node_property_predicates.
"""
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',
}
filename = os.path.join(RESOURCE_DIR, 'rdf', 'oban-test.nt')
source = RdfSource()
source.set_prefix_map(prefix_map)
source.set_node_property_predicates(node_property_predicates)
g = source.parse(filename=filename, format='nt')
nodes, edges = process_stream(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['frequencyOfPhenotype'] == 'HP:0040283'
def test_read_nt2():
"""
Read from an RDF N-Triple file using RdfSource.
This test also supplies the provided_by parameter.
"""
s = RdfSource()
g = s.parse(os.path.join(RESOURCE_DIR, 'rdf', 'test1.nt'),
provided_by='Test Dataset')
nodes, edges = process_stream(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['provided_by']
def test_read_nt4():
"""
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", "test3.nt"),
format="nt")
nodes, edges = load_graph_dictionary(g)
assert len(nodes.keys()) == 7
assert len(edges.keys()) == 6
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"
e2 = edges["ENSEMBL:ENSP0000000000001", "UniProtKB:X0000001"][0]
assert e2["subject"] == "ENSEMBL:ENSP0000000000001"
assert e2["object"] == "UniProtKB:X0000001"
assert e2["predicate"] == "biolink:same_as"
assert e2["relation"] == "owl:equivalentClass"
e3 = edges["ENSEMBL:ENSP0000000000001", "MONDO:0000001"][0]
assert e3["subject"] == "ENSEMBL:ENSP0000000000001"
assert e3["object"] == "MONDO:0000001"
assert e3["predicate"] == "biolink:treats"
assert e3["relation"] == "RO:0002606"