class TestGwasHaplotypeModel(unittest.TestCase):
"""
Test the modelling of a SNP to trait association
from sample GWAS catalog data
"""
def setUp(self):
self.source = GWASCatalog('rdf_graph', True)
self.test_data = {
'snp_label': 'rs1329573-?; rs7020413-?; rs3824344-?; rs3758171-?',
'chrom_num': '9;9;9;9',
'chrom_pos': '36998996;37002118;37000690;36997420',
'context':
'intron_variant; intron_variant; intron_variant; intron_variant',
'allele_freq': 'NR',
'trait': 'Intelligence',
'trait_uri': 'http://www.ebi.ac.uk/efo/EFO_0004337',
'pvalue': '0.00000004',
'merged': '0',
'snp_id_current': '',
'mapped_gene': 'PAX5; PAX5; PAX5; PAX5',
'snp_gene_nums': '',
'upstream_gene_num': '107986179',
'downstream_gene_num': '107986180',
'init_sample_desc':
'656 European ancestry individuals from ADHD families',
'replicated_sample_desc': 'NA',
'platform': 'Illumina [795637]',
'pubmed': '22449649'
}
def tearDown(self):
self.source = None
def test_snp_model(self):
"""
Test output model of _process_haplotype()
self._process_haplotype(
variant_curie, strongest_snp_risk_allele,
chrom_num, chrom_pos, context,
risk_allele_frequency, mapped_gene, so_ontology)
"""
variant_curie, variant_type = \
self.source._get_curie_and_type_from_id(self.test_data['snp_label'])
so_ontology = RDFGraph()
logger.info("Loading SO ontology in separate rdf graph")
so_ontology.parse(self.source.files['so']['url'], format='xml')
so_ontology.bind_all_namespaces()
logger.info("Finished loading SO ontology")
self.source._process_haplotype(
variant_curie, self.test_data['snp_label'],
self.test_data['chrom_num'], self.test_data['chrom_pos'],
self.test_data['context'], self.test_data['allele_freq'],
self.test_data['mapped_gene'], so_ontology)
sparql_query = """
SELECT ?snp
WHERE {
:haplotype_bcb627b1f64039b0 a OBO:GENO_0000871 ;
rdfs:label "rs1329573-?; rs7020413-?; rs3824344-?; rs3758171-?" ;
OBO:GENO_0000382 ?snp,
dbSNP:rs3758171,
dbSNP:rs3824344,
dbSNP:rs7020413 ;
OBO:GENO_0000418 <http://identifiers.org/hgnc/HGNC:8619> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
?snp a OBO:SO_0000694,
OBO:SO_0001627 ;
rdfs:label "rs1329573-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996-36998996-Region> ;
OBO:GENO_0000418 <http://identifiers.org/hgnc/HGNC:8619> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
dbSNP:rs3758171 a OBO:SO_0000694,
OBO:SO_0001627 ;
rdfs:label "rs3758171-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420-36997420-Region> ;
OBO:GENO_0000418 <http://identifiers.org/hgnc/HGNC:8619> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
dbSNP:rs3824344 a OBO:SO_0000694,
OBO:SO_0001627 ;
rdfs:label "rs3824344-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690-37000690-Region> ;
OBO:GENO_0000418 <http://identifiers.org/hgnc/HGNC:8619> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
dbSNP:rs7020413 a OBO:SO_0000694,
OBO:SO_0001627 ;
rdfs:label "rs7020413-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118-37002118-Region> ;
OBO:GENO_0000418 <http://identifiers.org/hgnc/HGNC:8619> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420-36997420-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996-36998996-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690-37000690-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118-37002118-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420> a faldo:Position ;
faldo:position 36997420 ;
faldo:reference OBO:CHR_GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996> a faldo:Position ;
faldo:position 36998996 ;
faldo:reference OBO:CHR_GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690> a faldo:Position ;
faldo:position 37000690 ;
faldo:reference OBO:CHR_GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118> a faldo:Position ;
faldo:position 37002118 ;
faldo:reference OBO:CHR_GRCh38chr9 .
}
"""
sparql_output = self.source.graph.query(sparql_query)
# Test that query passes and returns one row
results = list(sparql_output)
expected = [(URIRef(self.source.graph._getNode("dbSNP:rs1329573")), )]
self.assertEqual(results, expected)
class TestGwasSNPModel(unittest.TestCase):
"""
Test the modelling of a SNP to trait association
from sample GWAS catalog data
"""
def setUp(self):
self.source = GWASCatalog('rdf_graph', True)
self.test_data = {
'snp_label': 'rs1491921-C',
'chrom_num': '5',
'chrom_pos': '21259029',
'context': 'intergenic_variant',
'allele_freq': '0.013',
'trait': 'Diisocyanate-induced asthma',
'trait_uri':
'http://www.ebi.ac.uk/efo/EFO_0006995, http://www.ebi.ac.uk/efo/EFO_0003949',
'pvalue': '0.0000007',
'merged': '0',
'snp_id_current': '1491921',
'mapped_gene': 'LOC102723561 - GUSBP1',
'snp_gene_nums': '',
'upstream_gene_num': '107986179',
'downstream_gene_num': '107986180',
'init_sample_desc':
'74 European ancestry cases, 824 European ancestry controls',
'replicated_sample_desc': 'NA',
'platform': 'Illumina [1556551]',
'pubmed': '25918132'
}
def tearDown(self):
self.source = None
self.efo_ontology = None
def test_snp_type_resolution(self):
"""
Given the label: rs1491921-C
return dbSNP:rs1491921, snp
"""
variant_curie, variant_type = \
self.source._get_curie_and_type_from_id(self.test_data['snp_label'])
self.assertEqual(variant_curie, "dbSNP:rs1491921")
self.assertEqual(variant_type, 'snp')
def test_snp_model(self):
"""
Test output model of _add_snp_to_graph()
"""
variant_curie, variant_type = \
self.source._get_curie_and_type_from_id(self.test_data['snp_label'])
self.source._add_snp_to_graph(variant_curie,
self.test_data['snp_label'],
self.test_data['chrom_num'],
self.test_data['chrom_pos'],
self.test_data['context'],
self.test_data['allele_freq'])
sparql_query = """
SELECT ?snp
WHERE {
?snp a OBO:SO_0000694,
OBO:SO_0001628 ;
rdfs:label "rs1491921-C" ;
faldo:location
<https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029-21259029-Region> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 ;
dc:description "0.013 [risk allele frequency]" .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029-21259029-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029> a faldo:Position ;
faldo:position 21259029 ;
faldo:reference OBO:CHR_GRCh38chr5 .
}
"""
# To debug
#print(self.source.graph.serialize(format="turtle").decode("utf-8"))
#self.assertTrue(False)
sparql_output = self.source.graph.query(sparql_query)
# Test that query passes and returns one row
results = list(sparql_output)
expected = [(URIRef(self.source.graph._getNode("dbSNP:rs1491921")), )]
self.assertEqual(results, expected)
def test_snp_gene_relation(self):
"""
test the _add_snp_gene_relation function
:return:
"""
variant_curie, variant_type = \
self.source._get_curie_and_type_from_id(self.test_data['snp_label'])
self.source._add_snp_gene_relation(
variant_curie, self.test_data['snp_gene_nums'],
self.test_data['upstream_gene_num'],
self.test_data['downstream_gene_num'])
sparql_query = """
SELECT ?snp
WHERE {
?snp OBO:RO_0002528 <http://www.ncbi.nlm.nih.gov/gene/107986180> ;
OBO:RO_0002529 <http://www.ncbi.nlm.nih.gov/gene/107986179> .
}
"""
sparql_output = self.source.graph.query(sparql_query)
# Test that query passes and returns one row
results = list(sparql_output)
expected = [(URIRef(self.source.graph._getNode("dbSNP:rs1491921")), )]
self.assertEqual(results, expected)
def test_deprecated_snp(self):
"""
test the _add_deprecated_snp
:return:
"""
#fake data
snp_id_current = '12345'
merged = '1'
variant_curie, variant_type = \
self.source._get_curie_and_type_from_id(self.test_data['snp_label'])
self.source._add_deprecated_snp(variant_curie, snp_id_current, merged,
self.test_data['chrom_num'],
self.test_data['chrom_pos'])
sparql_query = """
SELECT ?snp
WHERE {
?snp a owl:NamedIndividual ;
OBO:IAO_0100001 dbSNP:rs12345 ;
owl:deprecated true .
dbSNP:rs12345 MONARCH:cliqueLeader true .
}
"""
sparql_output = self.source.graph.query(sparql_query)
# Test that query passes and returns one row
results = list(sparql_output)
expected = [(URIRef(self.source.graph._getNode("dbSNP:rs1491921")), )]
self.assertEqual(results, expected)
def test_snp_trait_association(self):
"""
test the _add_variant_trait_association
:return:
"""
efo_ontology = RDFGraph()
logger.info("Loading EFO ontology in separate rdf graph")
efo_ontology.parse(self.source.files['efo']['url'], format='xml')
efo_ontology.bind_all_namespaces()
logger.info("Finished loading EFO ontology")
variant_curie, variant_type = \
self.source._get_curie_and_type_from_id(self.test_data['snp_label'])
description = self.source._make_description(
self.test_data['trait'], self.test_data['init_sample_desc'],
self.test_data['replicated_sample_desc'],
self.test_data['platform'], self.test_data['pvalue'])
self.source._add_variant_trait_association(variant_curie,
self.test_data['trait_uri'],
efo_ontology,
self.test_data['pubmed'],
description)
sparql_query = """
SELECT ?snp
WHERE {{
<https://monarchinitiative.org/MONARCH_b46cdf48950cb00d> a OBAN:association ;
dc:description "{}" ;
OBO:RO_0002558 OBO:ECO_0000213 ;
dc:source PMID:25918132 ;
OBAN:association_has_object EFO:0003949 ;
OBAN:association_has_predicate OBO:RO_0002326 ;
OBAN:association_has_subject ?snp .
<https://monarchinitiative.org/MONARCH_70a05d8eb1c3d4b0> a OBAN:association ;
OBO:RO_0002558 OBO:ECO_0000213 ;
dc:source PMID:25918132 ;
OBAN:association_has_object EFO:0006995 ;
OBAN:association_has_predicate OBO:RO_0002326 ;
OBAN:association_has_subject ?snp .
EFO:0003949 a owl:Class ;
rdfs:label "eye color"^^xsd:string ;
rdfs:subClassOf UPHENO:0001001 .
?snp OBO:RO_0002326 EFO:0003949,
EFO:0006995 .
PMID:25918132 a OBO:IAO_0000013 .
}}
""".format(description)
sparql_output = self.source.graph.query(sparql_query)
# Test that query passes and returns one row
results = list(sparql_output)
expected = [(URIRef(self.source.graph._getNode("dbSNP:rs1491921")), )]
self.assertEqual(results, expected)
class TestGwasHaplotypeModel(unittest.TestCase):
"""
Test the modelling of a SNP to trait association
from sample GWAS catalog data
"""
def setUp(self):
self.test_util = TestUtils()
self.source = GWASCatalog('rdf_graph', True)
self.source.graph = RDFGraph(True)
self.test_data = {
'snp_label': 'rs1329573-?; rs7020413-?; rs3824344-?; rs3758171-?',
'chrom_num': '9;9;9;9',
'chrom_pos': '36998996;37002118;37000690;36997420',
'context': 'intron_variant; intron_variant; intron_variant; intron_variant',
'allele_freq': 'NR',
'trait': 'Intelligence',
'trait_uri': 'http://www.ebi.ac.uk/efo/EFO_0004337',
'pvalue': '0.00000004',
'merged': '0',
'snp_id_current': '',
'mapped_gene': 'PAX5; PAX5; PAX5; PAX5',
'snp_gene_nums': '',
'upstream_gene_num': '107986179',
'downstream_gene_num': '107986180',
'init_sample_desc': '656 European ancestry individuals from ADHD families',
'replicated_sample_desc': 'NA',
'platform': 'Illumina [795637]',
'pubmed': '22449649'
}
def tearDown(self):
self.source = None
def test_snp_model(self):
"""
Test output model of _process_haplotype()
self._process_haplotype(
variant_curie, strongest_snp_risk_allele,
chrom_num, chrom_pos, context,
risk_allele_frequency, mapped_gene, so_ontology)
"""
self.assertTrue(len(list(self.source.graph)) == 0)
variant_curie, variant_type = self.source._get_curie_and_type_from_id(
self.test_data['snp_label'])
so_ontology = RDFGraph()
LOG.info("Loading SO ontology in separate rdf graph")
so_ontology.parse(self.source.files['so']['url'], format='xml')
so_ontology.bind_all_namespaces()
LOG.info("Finished loading SO ontology")
self.source._process_haplotype(
variant_curie, self.test_data['snp_label'], self.test_data['chrom_num'],
self.test_data['chrom_pos'], self.test_data['context'],
self.test_data['allele_freq'], self.test_data['mapped_gene'], so_ontology)
triples = """
:haplotype_bb627b1f64039b0f751a a OBO:GENO_0000871 ;
rdfs:label "rs1329573-?; rs7020413-?; rs3824344-?; rs3758171-?" ;
OBO:GENO_0000382 dbSNP:rs1329573,
dbSNP:rs3758171,
dbSNP:rs3824344,
dbSNP:rs7020413 ;
OBO:SO_0001627 HGNC:8619 ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
dbSNP:rs1329573 a OBO:SO_0000694,
SO:0001627 ;
rdfs:label "rs1329573-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996-36998996-Region> ;
OBO:SO_0001627 HGNC:8619 ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
dbSNP:rs3758171 a OBO:SO_0000694,
OBO:SO_0001627 ;
rdfs:label "rs3758171-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420-36997420-Region> ;
OBO:SO_0001627 HGNC:8619 ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
dbSNP:rs3824344 a OBO:SO_0000694,
OBO:SO_0001627 ;
rdfs:label "rs3824344-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690-37000690-Region> ;
OBO:SO_0001627 HGNC:8619 ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
dbSNP:rs7020413 a OBO:SO_0000694,
OBO:SO_0001627 ;
rdfs:label "rs7020413-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118-37002118-Region> ;
OBO:SO_0001627 HGNC:8619 ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420-36997420-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996-36998996-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690-37000690-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118-37002118-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420> a faldo:Position ;
faldo:position 36997420 ;
faldo:reference OBO:CHR_GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996> a faldo:Position ;
faldo:position 36998996 ;
faldo:reference OBO:CHR_GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690> a faldo:Position ;
faldo:position 37000690 ;
faldo:reference OBO:CHR_GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118> a faldo:Position ;
faldo:position 37002118 ;
faldo:reference OBO:CHR_GRCh38chr9 .
"""
# dbg
# LOG.debug(
# "Reference graph: %s",
# self.source.graph.serialize(format="turtle").decode("utf-8"))
# Does not seem to acknowlage these constant triples
self.assertTrue(self.test_util.test_graph_equality(triples, self.source.graph))
class TestGwasSNPModel(unittest.TestCase):
"""
Test the modelling of a SNP to trait association
from sample GWAS catalog data
"""
def setUp(self):
self.test_util = TestUtils()
self.source = GWASCatalog('rdf_graph', True)
self.source.graph = RDFGraph(True) # Reset graph
self.source.graph.bind_all_namespaces()
self.test_data = {
'snp_label': 'rs1491921-C',
'chrom_num': '5',
'chrom_pos': '21259029',
'context': 'intergenic_variant',
'allele_freq': '0.013',
'trait': 'Diisocyanate-induced asthma',
'trait_uri': 'http://www.ebi.ac.uk/efo/EFO_0006995, http://www.ebi.ac.uk/efo/EFO_0003949',
'pvalue': '0.0000007',
'merged': '0',
'snp_id_current': '1491921',
'mapped_gene': 'LOC102723561 - GUSBP1',
'snp_gene_nums': '',
'upstream_gene_num': '107986179',
'downstream_gene_num': '107986180',
'init_sample_desc': '74 European ancestry cases, 824 European ancestry controls',
'replicated_sample_desc': 'NA',
'platform': 'Illumina [1556551]',
'pubmed': '25918132'
}
def tearDown(self):
self.source = None
self.efo_ontology = None
def test_snp_type_resolution(self):
"""
Given the label: rs1491921-C
return dbSNP:rs1491921, snp
"""
self.assertTrue(len(list(self.source.graph)) == 0)
variant_curie, variant_type = self.source._get_curie_and_type_from_id(
self.test_data['snp_label'])
self.assertEqual(variant_curie, "dbSNP:rs1491921")
self.assertEqual(variant_type, 'snp')
def test_snp_model(self):
"""
Test output model of _add_snp_to_graph()
"""
self.assertTrue(len(list(self.source.graph)) == 0)
variant_curie, variant_type = self.source._get_curie_and_type_from_id(
self.test_data['snp_label'])
self.source._add_snp_to_graph(
variant_curie, self.test_data['snp_label'], self.test_data['chrom_num'],
self.test_data['chrom_pos'], self.test_data['context'],
self.test_data['allele_freq'])
triples = """
dbSNP:rs1491921 a OBO:SO_0000694, OBO:SO_0001628 ;
rdfs:label "rs1491921-C" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029-21259029-Region> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 ;
dc:description "0.013 [risk allele frequency]" .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029-21259029-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029> a faldo:Position ;
faldo:position 21259029 ;
faldo:reference OBO:CHR_GRCh38chr5 .
"""
# To debug
# print(self.source.graph.serialize(format="turtle").decode("utf-8"))
# self.assertTrue(False)
# dbg
# LOG.debug(
# "Reference graph: %s",
# self.source.graph.serialize(format="turtle").decode("utf-8"))
self.assertTrue(self.test_util.test_graph_equality(triples, self.source.graph))
def test_snp_gene_relation(self):
"""
test the _add_snp_gene_relation function
:return:
"""
self.assertTrue(len(list(self.source.graph)) == 0)
variant_curie, variant_type = self.source._get_curie_and_type_from_id(
self.test_data['snp_label'])
self.source._add_snp_gene_relation(
variant_curie, self.test_data['snp_gene_nums'],
self.test_data['upstream_gene_num'],
self.test_data['downstream_gene_num'])
triples = """
dbSNP:rs1491921 OBO:RO_0002528 NCBIGene:107986180 ;
OBO:RO_0002529 NCBIGene:107986179 .
"""
self.assertTrue(self.test_util.test_graph_equality(triples, self.source.graph))
def test_deprecated_snp(self):
"""
test the _add_deprecated_snp
:return:
"""
self.assertTrue(len(list(self.source.graph)) == 0)
# fake data
snp_id_current = '12345'
merged = '1'
variant_curie, variant_type = self.source._get_curie_and_type_from_id(
self.test_data['snp_label'])
self.source._add_deprecated_snp(
variant_curie, snp_id_current, merged,
self.test_data['chrom_num'], self.test_data['chrom_pos'])
triples = """
dbSNP:rs1491921 a owl:NamedIndividual ;
OBO:IAO_0100001 dbSNP:rs12345 ;
owl:deprecated true .
dbSNP:rs12345 MONARCH:cliqueLeader true .
"""
self.assertTrue(self.test_util.test_graph_equality(triples, self.source.graph))
def test_snp_trait_association(self):
"""
test the _add_variant_trait_association
:return:
"""
self.assertTrue(len(list(self.source.graph)) == 0)
efo_ontology = RDFGraph()
LOG.info("Loading EFO ontology in separate rdf graph")
efo_ontology.parse(self.source.files['efo']['url'], format='xml')
efo_ontology.bind_all_namespaces()
LOG.info("Finished loading EFO ontology")
variant_curie, variant_type = self.source._get_curie_and_type_from_id(
self.test_data['snp_label'])
description = self.source._make_description(
self.test_data['trait'], self.test_data['init_sample_desc'],
self.test_data['replicated_sample_desc'],
self.test_data['platform'], self.test_data['pvalue'])
self.source._add_variant_trait_association(
variant_curie, self.test_data['trait_uri'], efo_ontology,
self.test_data['pubmed'], description)
triples = """
MONARCH:bffc7a930c08cc8fe931 a OBAN:association ;
dc:description "{0}" ;
OBO:RO_0002558 OBO:ECO_0000213 ;
dc:source PMID:25918132 ;
OBAN:association_has_object EFO:0003949 ;
OBAN:association_has_predicate RO:0003304 ;
OBAN:association_has_subject dbSNP:rs1491921 .
MONARCH:bff9b97458d67ed7f517 a OBAN:association ;
dc:description "{0}" ;
OBO:RO_0002558 OBO:ECO_0000213 ;
dc:source PMID:25918132 ;
OBAN:association_has_object EFO:0006995 ;
OBAN:association_has_predicate RO:0003304 ;
OBAN:association_has_subject dbSNP:rs1491921 .
EFO:0003949 a owl:Class ;
rdfs:label "eye color"^^xsd:string ;
rdfs:subClassOf UPHENO:0001001 .
dbSNP:rs1491921 RO:0003304 EFO:0003949,
EFO:0006995 .
PMID:25918132 a OBO:IAO_0000013 .
""".format(description)
# dbg
# LOG.debug(
# "Reference graph: %s",
# self.source.graph.serialize(format="turtle").decode("utf-8"))
self.assertTrue(self.test_util.test_graph_equality(triples, self.source.graph))
class TestGwasHaplotypeModel(unittest.TestCase):
"""
Test the modelling of a SNP to trait association
from sample GWAS catalog data
"""
def setUp(self):
self.test_util = TestUtils()
self.source = GWASCatalog('rdf_graph', True)
self.source.graph = RDFGraph(True)
self.test_data = {
'snp_label': 'rs1329573-?; rs7020413-?; rs3824344-?; rs3758171-?',
'chrom_num': '9;9;9;9',
'chrom_pos': '36998996;37002118;37000690;36997420',
'context':
'intron_variant; intron_variant; intron_variant; intron_variant',
'allele_freq': 'NR',
'trait': 'Intelligence',
'trait_uri': 'http://www.ebi.ac.uk/efo/EFO_0004337',
'pvalue': '0.00000004',
'merged': '0',
'snp_id_current': '',
'mapped_gene': 'PAX5; PAX5; PAX5; PAX5',
'snp_gene_nums': '',
'upstream_gene_num': '107986179',
'downstream_gene_num': '107986180',
'init_sample_desc':
'656 European ancestry individuals from ADHD families',
'replicated_sample_desc': 'NA',
'platform': 'Illumina [795637]',
'pubmed': '22449649'
}
def tearDown(self):
self.source = None
def test_snp_model(self):
"""
Test output model of _process_haplotype()
self._process_haplotype(
variant_curie, strongest_snp_risk_allele,
chrom_num, chrom_pos, context,
risk_allele_frequency, mapped_gene, so_ontology)
"""
self.assertTrue(len(list(self.source.graph)) == 0)
variant_curie, variant_type = self.source._get_curie_and_type_from_id(
self.test_data['snp_label'])
so_ontology = RDFGraph()
LOG.info("Loading SO ontology in separate rdf graph")
so_ontology.parse(self.source.files['so']['url'], format='xml')
so_ontology.bind_all_namespaces()
LOG.info("Finished loading SO ontology")
self.source._process_haplotype(
variant_curie, self.test_data['snp_label'],
self.test_data['chrom_num'], self.test_data['chrom_pos'],
self.test_data['context'], self.test_data['allele_freq'],
self.test_data['mapped_gene'], so_ontology)
triples = """
:haplotype_bb627b1f64039b0f751a a SO:0001024 ;
rdfs:label "rs1329573-?; rs7020413-?; rs3824344-?; rs3758171-?" ;
GENO:0000382 dbSNP:rs1329573,
dbSNP:rs3758171,
dbSNP:rs3824344,
dbSNP:rs7020413 ;
GENO:0000418 HGNC:8619 ;
RO:0002162 NCBITaxon:9606 .
dbSNP:rs1329573 a SO:0000694,
SO:0001627 ;
rdfs:label "rs1329573-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/b3fad5df82cdfb283329> ;
GENO:0000418 HGNC:8619 ;
RO:0002162 NCBITaxon:9606 .
dbSNP:rs3758171 a SO:0000694,
SO:0001627 ;
rdfs:label "rs3758171-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/b25a2da36647bdd71be3> ;
GENO:0000418 HGNC:8619 ;
RO:0002162 NCBITaxon:9606 .
dbSNP:rs3824344 a SO:0000694,
OBO:SO_0001627 ;
rdfs:label "rs3824344-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/b096a3e94e32fe23374a> ;
GENO:0000418 HGNC:8619 ;
RO:0002162 NCBITaxon:9606 .
dbSNP:rs7020413 a SO:0000694,
SO:0001627 ;
rdfs:label "rs7020413-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/bbb252d9b6cd02e9880a> ;
GENO:0000418 HGNC:8619 ;
RO:0002162 NCBITaxon:9606 .
<https://monarchinitiative.org/.well-known/genid/b25a2da36647bdd71be3> a faldo:Region ;
rdfs:label "GRCh38chr9-36997420-36997420-Region";
faldo:begin <https://monarchinitiative.org/.well-known/genid/b21985847fe0774084eb> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/b21985847fe0774084eb> .
<https://monarchinitiative.org/.well-known/genid/b3fad5df82cdfb283329> a faldo:Region ;
rdfs:label "GRCh38chr9-36998996-36998996-Region";
faldo:begin <https://monarchinitiative.org/.well-known/genid/b55051762f8d5a3dbeb5> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/b55051762f8d5a3dbeb5> .
<https://monarchinitiative.org/.well-known/genid/b096a3e94e32fe23374a> a faldo:Region ;
rdfs:label "GRCh38chr9-37000690-37000690-Region";
faldo:begin <https://monarchinitiative.org/.well-known/genid/b5d61dbc7958a979d046> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/b5d61dbc7958a979d046> .
<https://monarchinitiative.org/.well-known/genid/bbb252d9b6cd02e9880a> a faldo:Region ;
rdfs:label "GRCh38chr9-37002118-37002118-Region";
faldo:begin <https://monarchinitiative.org/.well-known/genid/bb870c3d7606a3e0fc3c> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/bb870c3d7606a3e0fc3c> .
<https://monarchinitiative.org/.well-known/genid/b21985847fe0774084eb> a faldo:Position ;
rdfs:label "GRCh38chr9-36997420";
faldo:position 36997420 ;
faldo:reference OBO:CHR_GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/b55051762f8d5a3dbeb5> a faldo:Position ;
rdfs:label "GRCh38chr9-36998996";
faldo:position 36998996 ;
faldo:reference CHR:GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/b5d61dbc7958a979d046> a faldo:Position ;
rdfs:label "GRCh38chr9-37000690";
faldo:position 37000690 ;
faldo:reference CHR:GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/bb870c3d7606a3e0fc3c> a faldo:Position ;
rdfs:label "GRCh38chr9-37002118";
faldo:position 37002118 ;
faldo:reference CHR:GRCh38chr9 .
"""
# dbg
LOG.debug("Reference graph: %s",
self.source.graph.serialize(format="turtle").decode("utf-8"))
self.assertTrue(
self.test_util.test_graph_equality(triples, self.source.graph))
class TestGwasSNPModel(unittest.TestCase):
"""
Test the modelling of a SNP to trait association
from sample GWAS catalog data
"""
def setUp(self):
self.source = GWASCatalog('rdf_graph', True)
self.test_data = {
'snp_label': 'rs1491921-C',
'chrom_num': '5',
'chrom_pos': '21259029',
'context': 'intergenic_variant',
'allele_freq': '0.013',
'trait': 'Diisocyanate-induced asthma',
'trait_uri': 'http://www.ebi.ac.uk/efo/EFO_0006995, http://www.ebi.ac.uk/efo/EFO_0003949',
'pvalue': '0.0000007',
'merged': '0',
'snp_id_current': '1491921',
'mapped_gene': 'LOC102723561 - GUSBP1',
'snp_gene_nums': '',
'upstream_gene_num': '107986179',
'downstream_gene_num': '107986180',
'init_sample_desc': '74 European ancestry cases, 824 European ancestry controls',
'replicated_sample_desc': 'NA',
'platform': 'Illumina [1556551]',
'pubmed': '25918132'
}
def tearDown(self):
self.source = None
self.efo_ontology = None
def test_snp_type_resolution(self):
"""
Given the label: rs1491921-C
return dbSNP:rs1491921, snp
"""
variant_curie, variant_type = \
self.source._get_curie_and_type_from_id(self.test_data['snp_label'])
self.assertEqual(variant_curie, "dbSNP:rs1491921")
self.assertEqual(variant_type, 'snp')
def test_snp_model(self):
"""
Test output model of _add_snp_to_graph()
"""
variant_curie, variant_type = \
self.source._get_curie_and_type_from_id(self.test_data['snp_label'])
self.source._add_snp_to_graph(
variant_curie, self.test_data['snp_label'], self.test_data['chrom_num'],
self.test_data['chrom_pos'], self.test_data['context'],
self.test_data['allele_freq'])
sparql_query = """
SELECT ?snp
WHERE {
?snp a OBO:SO_0000694,
OBO:SO_0001628 ;
rdfs:label "rs1491921-C" ;
faldo:location
<https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029-21259029-Region> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 ;
dc:description "0.013 [risk allele frequency]" .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029-21259029-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029> a faldo:Position ;
faldo:position 21259029 ;
faldo:reference OBO:CHR_GRCh38chr5 .
}
"""
# To debug
#print(self.source.graph.serialize(format="turtle").decode("utf-8"))
#self.assertTrue(False)
sparql_output = self.source.graph.query(sparql_query)
# Test that query passes and returns one row
results = list(sparql_output)
expected = [(URIRef(self.source.graph._getNode("dbSNP:rs1491921")),)]
self.assertEqual(results, expected)
def test_snp_gene_relation(self):
"""
test the _add_snp_gene_relation function
:return:
"""
variant_curie, variant_type = \
self.source._get_curie_and_type_from_id(self.test_data['snp_label'])
self.source._add_snp_gene_relation(
variant_curie, self.test_data['snp_gene_nums'],
self.test_data['upstream_gene_num'],
self.test_data['downstream_gene_num'])
sparql_query = """
SELECT ?snp
WHERE {
?snp OBO:RO_0002528 <http://www.ncbi.nlm.nih.gov/gene/107986180> ;
OBO:RO_0002529 <http://www.ncbi.nlm.nih.gov/gene/107986179> .
}
"""
sparql_output = self.source.graph.query(sparql_query)
# Test that query passes and returns one row
results = list(sparql_output)
expected = [(URIRef(self.source.graph._getNode("dbSNP:rs1491921")),)]
self.assertEqual(results, expected)
def test_deprecated_snp(self):
"""
test the _add_deprecated_snp
:return:
"""
#fake data
snp_id_current = '12345'
merged = '1'
variant_curie, variant_type = \
self.source._get_curie_and_type_from_id(self.test_data['snp_label'])
self.source._add_deprecated_snp(
variant_curie, snp_id_current, merged,
self.test_data['chrom_num'], self.test_data['chrom_pos'])
sparql_query = """
SELECT ?snp
WHERE {
?snp a owl:NamedIndividual ;
OBO:IAO_0100001 dbSNP:rs12345 ;
owl:deprecated true .
dbSNP:rs12345 MONARCH:cliqueLeader true .
}
"""
sparql_output = self.source.graph.query(sparql_query)
# Test that query passes and returns one row
results = list(sparql_output)
expected = [(URIRef(self.source.graph._getNode("dbSNP:rs1491921")),)]
self.assertEqual(results, expected)
def test_snp_trait_association(self):
"""
test the _add_variant_trait_association
:return:
"""
efo_ontology = RDFGraph()
logger.info("Loading EFO ontology in separate rdf graph")
efo_ontology.parse(self.source.files['efo']['url'], format='xml')
efo_ontology.bind_all_namespaces()
logger.info("Finished loading EFO ontology")
variant_curie, variant_type = \
self.source._get_curie_and_type_from_id(self.test_data['snp_label'])
description = self.source._make_description(
self.test_data['trait'], self.test_data['init_sample_desc'],
self.test_data['replicated_sample_desc'],
self.test_data['platform'], self.test_data['pvalue'])
self.source._add_variant_trait_association(
variant_curie, self.test_data['trait_uri'], efo_ontology,
self.test_data['pubmed'], description)
sparql_query = """
SELECT ?snp
WHERE {{
<https://monarchinitiative.org/MONARCH_b46cdf48950cb00d> a OBAN:association ;
dc:description "{}" ;
OBO:RO_0002558 OBO:ECO_0000213 ;
dc:source PMID:25918132 ;
OBAN:association_has_object EFO:0003949 ;
OBAN:association_has_predicate OBO:RO_0002326 ;
OBAN:association_has_subject ?snp .
<https://monarchinitiative.org/MONARCH_70a05d8eb1c3d4b0> a OBAN:association ;
OBO:RO_0002558 OBO:ECO_0000213 ;
dc:source PMID:25918132 ;
OBAN:association_has_object EFO:0006995 ;
OBAN:association_has_predicate OBO:RO_0002326 ;
OBAN:association_has_subject ?snp .
EFO:0003949 a owl:Class ;
rdfs:label "eye color"^^xsd:string ;
rdfs:subClassOf UPHENO:0001001 .
?snp OBO:RO_0002326 EFO:0003949,
EFO:0006995 .
PMID:25918132 a OBO:IAO_0000013 .
}}
""".format(description)
sparql_output = self.source.graph.query(sparql_query)
# Test that query passes and returns one row
results = list(sparql_output)
expected = [(URIRef(self.source.graph._getNode("dbSNP:rs1491921")),)]
self.assertEqual(results, expected)
class TestGwasHaplotypeModel(unittest.TestCase):
"""
Test the modelling of a SNP to trait association
from sample GWAS catalog data
"""
def setUp(self):
self.source = GWASCatalog('rdf_graph', True)
self.test_data = {
'snp_label': 'rs1329573-?; rs7020413-?; rs3824344-?; rs3758171-?',
'chrom_num': '9;9;9;9',
'chrom_pos': '36998996;37002118;37000690;36997420',
'context': 'intron_variant; intron_variant; intron_variant; intron_variant',
'allele_freq': 'NR',
'trait': 'Intelligence',
'trait_uri': 'http://www.ebi.ac.uk/efo/EFO_0004337',
'pvalue': '0.00000004',
'merged': '0',
'snp_id_current': '',
'mapped_gene': 'PAX5; PAX5; PAX5; PAX5',
'snp_gene_nums': '',
'upstream_gene_num': '107986179',
'downstream_gene_num': '107986180',
'init_sample_desc': '656 European ancestry individuals from ADHD families',
'replicated_sample_desc': 'NA',
'platform': 'Illumina [795637]',
'pubmed': '22449649'
}
def tearDown(self):
self.source = None
def test_snp_model(self):
"""
Test output model of _process_haplotype()
self._process_haplotype(
variant_curie, strongest_snp_risk_allele,
chrom_num, chrom_pos, context,
risk_allele_frequency, mapped_gene, so_ontology)
"""
variant_curie, variant_type = \
self.source._get_curie_and_type_from_id(self.test_data['snp_label'])
so_ontology = RDFGraph()
logger.info("Loading SO ontology in separate rdf graph")
so_ontology.parse(self.source.files['so']['url'], format='xml')
so_ontology.bind_all_namespaces()
logger.info("Finished loading SO ontology")
self.source._process_haplotype(
variant_curie, self.test_data['snp_label'], self.test_data['chrom_num'],
self.test_data['chrom_pos'], self.test_data['context'],
self.test_data['allele_freq'], self.test_data['mapped_gene'], so_ontology)
sparql_query = """
SELECT ?snp
WHERE {
:haplotype_bcb627b1f64039b0 a OBO:GENO_0000871 ;
rdfs:label "rs1329573-?; rs7020413-?; rs3824344-?; rs3758171-?" ;
OBO:GENO_0000382 ?snp,
dbSNP:rs3758171,
dbSNP:rs3824344,
dbSNP:rs7020413 ;
OBO:GENO_0000418 <http://identifiers.org/hgnc/HGNC:8619> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
?snp a OBO:SO_0000694,
OBO:SO_0001627 ;
rdfs:label "rs1329573-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996-36998996-Region> ;
OBO:GENO_0000418 <http://identifiers.org/hgnc/HGNC:8619> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
dbSNP:rs3758171 a OBO:SO_0000694,
OBO:SO_0001627 ;
rdfs:label "rs3758171-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420-36997420-Region> ;
OBO:GENO_0000418 <http://identifiers.org/hgnc/HGNC:8619> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
dbSNP:rs3824344 a OBO:SO_0000694,
OBO:SO_0001627 ;
rdfs:label "rs3824344-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690-37000690-Region> ;
OBO:GENO_0000418 <http://identifiers.org/hgnc/HGNC:8619> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
dbSNP:rs7020413 a OBO:SO_0000694,
OBO:SO_0001627 ;
rdfs:label "rs7020413-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118-37002118-Region> ;
OBO:GENO_0000418 <http://identifiers.org/hgnc/HGNC:8619> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420-36997420-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996-36998996-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690-37000690-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118-37002118-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420> a faldo:Position ;
faldo:position 36997420 ;
faldo:reference OBO:CHR_GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996> a faldo:Position ;
faldo:position 36998996 ;
faldo:reference OBO:CHR_GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690> a faldo:Position ;
faldo:position 37000690 ;
faldo:reference OBO:CHR_GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118> a faldo:Position ;
faldo:position 37002118 ;
faldo:reference OBO:CHR_GRCh38chr9 .
}
"""
sparql_output = self.source.graph.query(sparql_query)
# Test that query passes and returns one row
results = list(sparql_output)
expected = [(URIRef(self.source.graph._getNode("dbSNP:rs1329573")),)]
self.assertEqual(results, expected)
