def test_rdf_gxa_dex_levels(self):
cond_labels = set()
rdf = rdf_gxa_namespaces()
rdf += rdf_gxa_dex_levels("E-MTAB-4289", "RNASeq", None, cond_labels,
GxaTest.gene_filter)
log.info("rdf_gxa_dex_levels() test output (truncated):\n%s\n\n",
rdf[0:4000])
log.info("rdf_gxa_dex_levels(), returned conditions: %s", cond_labels)
graph = rdflib.Graph()
graph.parse(data=rdf, format="turtle")
self.assert_rdf(graph,
"ASK { bkr:gene_ensrna050013890 a bioschema:Gene }",
"Test gene ENSRNA050013890 not stated!")
self.assert_rdf(
graph,
"ASK { bkr:gene_ensrna050013890 schema:identifier 'ENSRNA050013890' }",
"ENSRNA050013890 identifier not stated!")
self.assert_rdf(
graph,
"ASK { bkr:gene_ensrna050013890 rdfs:label 'LSU_rRNA_eukarya'. }",
"ENSRNA050013890 rdfs:label not stated!")
cond_uri = "bkr:gxaexp_E-MTAB-4289_traescs7d02g366500_blumeria_graminis_0x3B_72_hour_vs_control"
self.assert_rdf(
graph, f"""ASK {{ {cond_uri} a rdfs:Statement;
rdf:subject bkr:gene_traescs7d02g366500;
rdf:predicate bioschema:expressedIn;
rdf:object bkr:cond_blumeria_graminis_0x3B_72_hour;
}}""", f"{cond_uri} not stated!")
self.assert_rdf(
graph,
"ASK { bkr:gene_traescs7d02g366500 bioschema:expressedIn bkr:cond_blumeria_graminis_0x3B_72_hour. }",
f"{cond_uri} not stated (summary statement)!")
self.assert_rdf(graph, f"ASK {{ {cond_uri} agri:log2FoldChange 2.2 }}",
f"{cond_uri}'s fold-change not stated!")
self.assert_rdf(
graph, f"""ASK {{ {cond_uri} agri:pvalue ?pvalue.
FILTER ( ?pvalue < 0.05 ) }}""",
f"{cond_uri}'s pvalue not stated or bad pvalue!")
self.assert_rdf(
graph, f"ASK {{ {cond_uri} agri:evidence bkr:exp_E-MTAB-4289 }}",
f"{cond_uri}'s evidence not stated!")
self.assert_rdf(
graph, f"ASK {{ {cond_uri} agri:baseCondition bkr:cond_control }}",
f"{cond_uri}'s base condition not stated!")
self.assertEqual(
set([
'control', 'Blumeria graminis; 24 hour',
'Blumeria graminis; 72 hour'
]), cond_labels, "Wrong set of conditions returned!")
def test_rdf_gxa_tpm_levels(self):
cond_labels = set()
rdf = rdf_gxa_namespaces()
rdf += rdf_gxa_tpm_levels("E-MTAB-4484", None, cond_labels,
GxaTest.gene_filter)
log.info("rdf_gxa_tpm_levels() test output (truncated):\n%s\n\n",
rdf[0:4000])
log.info("rdf_gxa_tpm_levels(), returned conditions: %s", cond_labels)
graph = rdflib.Graph()
graph.parse(data=rdf, format="turtle")
self.assert_rdf(
graph, "ASK { bkr:gene_traescs7a02g356100 a bioschema:Gene }",
"Test gene TRAESCS7A02G356100 not stated!")
self.assert_rdf(
graph,
"ASK { bkr:gene_traescs7a02g356100 schema:identifier 'TRAESCS7A02G356100' }",
"TRAESCS7A02G356100 identifier not stated!")
self.assert_rdf(
graph, "ASK { bkr:gene_traescs1a02g115900 rdfs:label 'ALI1'. }",
"traescs1a02g115900 rdfs:label not stated!")
self.assert_rdf(
graph,
"ASK { bkr:gxaexp_E-MTAB-4484_traescs7a02g356100_whole_plant_fruit_formation_stage_30_to_50_0x25_0x2C_leaf a rdfs:Statement }",
"traescs7a02g356100/stage-30-50 not stated!")
self.assert_rdf(
graph,
"ASK { bkr:gxaexp_E-MTAB-4484_traescs7a02g356100_whole_plant_fruit_formation_stage_30_to_50_0x25_0x2C_leaf agri:tpmCount 17.0 }",
"traescs7a02g356100/stage-30-50 without TPM count!")
self.assert_rdf(
graph,
"ASK { bkr:gxaexp_E-MTAB-4484_traescs7a02g356100_whole_plant_fruit_formation_stage_30_to_50_0x25_0x2C_leaf agri:tpmCount 17.0 }",
"traescs7a02g356100/stage-30-50 wrong or no TPM count!")
self.assert_rdf(
graph,
"ASK { bkr:gxaexp_E-MTAB-4484_traescs7a02g356100_whole_plant_fruit_formation_stage_30_to_50_0x25_0x2C_leaf agri:ordinalTpm 'medium' }",
"traescs7a02g356100/stage-30-50 wrong or no ordinal TPM!")
self.assert_rdf(
graph,
"""ASK { bkr:gxaexp_E-MTAB-4484_traescs7a02g356100_whole_plant_fruit_formation_stage_30_to_50_0x25_0x2C_leaf
rdf:subject bkr:gene_traescs7a02g356100;
rdf:predicate bioschema:expressedIn;
rdf:object bkr:cond_whole_plant_fruit_formation_stage_30_to_50_0x25_0x2C_leaf;
agri:evidence bkr:exp_E-MTAB-4484. }""",
"traescs7a02g356100/stage-30-50 wrong statements!")
self.assertTrue(
"whole plant fruit formation stage 30 to 50%, leaf" in cond_labels,
"Condition not in the result!")
def test_rdf_gxa_dex_levels_microarray(self):
cond_labels = set()
rdf = rdf_gxa_namespaces()
rdf += rdf_gxa_dex_levels("E-MTAB-8326", "Microarray", None,
cond_labels, GxaTest.gene_filter)
log.info(
"rdf_gxa_dex_levels(Microarray) test output (truncated):\n%s\n\n",
rdf[0:4000])
log.info("rdf_gxa_dex_levels(Microarray), returned conditions: %s",
cond_labels)
graph = rdflib.Graph()
graph.parse(data=rdf, format="turtle")
self.assert_rdf(
graph, """ASK {
?dex a rdfs:Statement;
rdf:subject ?gene;
rdf:predicate bioschema:expressedIn;
rdf:object bkr:cond_vip2_overexpression;
agri:baseCondition bkr:cond_wild_type_genotype;
agri:log2FoldChange ?fc;
agri:pvalue ?pvalue;
agri:evidence bkr:exp_E-MTAB-8326;
agri:timePoint bkr:cond_0_hours
.
FILTER ( ?pvalue < 0.05 )
FILTER ( ABS( ?fc ) > 1 )
?gene a bioschema:Gene;
schema:identifier "AT1G01010";
rdfs:label "NAC001"
.
}""", "DEX statements about 0 hrs not found!")
self.assert_rdf(
graph, """ASK {
?dex a rdfs:Statement;
rdf:subject ?gene;
rdf:predicate bioschema:expressedIn;
rdf:object ?cond;
agri:baseCondition ?baseline;
agri:log2FoldChange ?fc;
agri:pvalue ?pvalue;
agri:evidence bkr:exp_E-MTAB-8326;
agri:timePoint bkr:cond_72_hours
.
FILTER ( ?pvalue < 0.05 )
FILTER ( ABS( ?fc ) > 1 )
}""", "DEX statements about 72 hrs not found!")
def test_rdf_ae_experiments(self):
rdf = rdf_gxa_namespaces()
rdf += rdf_ae_experiment(AeTest.ae_exps['E-MTAB-8326'], None)
rdf += rdf_ae_experiment(AeTest.ae_exps['E-GEOD-25759'], None)
log.info("rdf_ae_experiment() test output (truncated):\n%s\n\n",
rdf[0:4000])
graph = rdflib.Graph()
graph.parse(data=rdf, format="turtle")
self.assert_rdf(
graph, """ASK {
bkr:exp_E-MTAB-8326 a bioschema:Study;
schema:identifier "E-MTAB-8326";
dc:title ?title;
schema:description ?descr;
schema:datePublished "2019-09-26";
schema:additionalProperty bkr:gxa_analysis_type_differential.
FILTER ( REGEX ( ?title, "Transcriptome analysis of Arabidopsis VIRE2-INTERACTING PROTEIN2" ) )
FILTER ( REGEX ( ?descr, "C-terminal NOT2 domain of VIP2 interacts with VirE2" ) )
}""", "Basic RDF data about E-MTAB-8326 not found!")
self.assert_rdf(
graph, """ASK {
bkr:exp_E-GEOD-25759 schema:additionalProperty bkr:specie_triticum_aestivum.
bkr:specie_triticum_aestivum a schema:PropertyValue;
schema:propertyID "organism";
schema:value "Triticum aestivum".
}""", "Specie RDF data about E-GEOD-25759 not found!")
self.assert_rdf(
graph, """ASK {
bkr:exp_E-GEOD-25759 schema:subjectOf bkr:pmid_21981858.
bkr:pmid_21981858 a agri:ScholarlyPublication;
dc:title ?title;
agri:authorsList ?authors;
agri:pmedId "21981858"
.
FILTER ( REGEX ( ?title, "Effect of the down-regulation of the high Grain Protein Content" ) )
FILTER ( REGEX ( ?authors, "Cantu D, Pearce SP, Distelfeld A" ) )
}""", "Publication RDF data about E-GEOD-25759 not found!")
def gxa_rdf_all(exp_js: dict, out=stdout, target_gene_ids: set = None):
if not out: out = io.StringIO()
print(rdf_gxa_namespaces(), file=out)
rdf_ae_experiment(exp_js, out)
exp_acc = exp_js['accession']
ae_tech_type = exp_js["aeTechnologyType"]
gxa_analysis_type = exp_js['gxaAnalysisType']
cond_labels = set()
if "Baseline" == gxa_analysis_type:
rdf_gxa_tpm_levels(exp_acc, out, cond_labels, target_gene_ids)
else:
rdf_gxa_dex_levels(exp_acc, ae_tech_type, out, cond_labels,
target_gene_ids)
rdf_gxa_conditions(cond_labels, out)
if (type(out) == io.StringIO): return out.getvalue()
def test_gxa_conditions(self):
cond_labels = [
'pericarp', 'Seed growth', '10 days after anthesis', '24 hours'
]
rdf = rdf_gxa_namespaces()
rdf += rdf_gxa_conditions(cond_labels, None)
log.info("rdf_gxa_conditions() test output:\n%s", rdf)
graph = rdflib.Graph()
graph.parse(data=rdf, format="turtle")
probes = [
("bkr:cond_pericarp a agri:StudyFactor; schema:name 'pericarp'",
"Cannot find RDF for pericarp!"),
("bkr:cond_seed_growth a agri:StudyFactor; schema:name 'Seed growth'",
"Cannot find RDF for seed growth!"),
("bkr:cond_10_days_after_anthesis a agri:StudyFactor; schema:name '10 days after anthesis'",
"Cannot find RDF for 10 days after anthesis!"),
("bkr:cond_pericarp dc:type <http://aims.fao.org/aos/agrovoc/c_25199>",
"Cannot find agrovoc:c_25199 for pericarp!"),
("<http://aims.fao.org/aos/agrovoc/c_25199> schema:name \"pericarp\"",
"Cannot find schema:name for pericarp!"),
("<http://purl.obolibrary.org/obo/PO_0009084> schema:identifier \"PO_0009084\"",
"Cannot find schema:name for pericarp!"),
("<http://knetminer.org/data/rdf/resources/plantontologyterm_po_0009010> schema:sameAs <http://purl.obolibrary.org/obo/PO_0009010>",
"Cannot fine knetminer/PO sameAs annotation for PO:0009010!"),
("bkr:cond_10_days_after_anthesis dc:type <http://aims.fao.org/aos/agrovoc/c_2992>",
"Cannot find 'flowering' annotation for anthesis entry!"),
("bkr:cond_10_days_after_anthesis dc:type <http://www.cropontology.org/rdf/CO_330:0000155>",
"Cannot find 'days' annotation for anthesis entry!"),
("""
bkr:cond_24_hours a agri:StudyFactor;
schema:name "24 hours";
schema:value 24;
schema:unitText "hours"
.
""", "Cannot find right annotations about the 24 hours time point!")
]
for (rdf, msg) in probes:
self.assert_rdf(graph, "ASK { %s }" % rdf, msg)
def test_extended_baseline(self):
cond_labels = set()
rdf = rdf_gxa_namespaces()
rdf += rdf_gxa_dex_levels("E-MTAB-8073", "RNASeq", None, cond_labels,
GxaTest.gene_filter)
log.info(
"rdf_gxa_dex_levels(Microarray) test output (truncated):\n%s\n\n",
rdf[0:4000])
log.info("rdf_gxa_dex_levels(Microarray), returned conditions: %s",
cond_labels)
graph = rdflib.Graph()
graph.parse(data=rdf, format="turtle")
self.assert_rdf(
graph, """ASK {
?dex a rdfs:Statement;
rdf:subject ?gene;
rdf:predicate bioschema:expressedIn;
rdf:object bkr:cond_sodium_chloride_0x3B_150_millimolar;
agri:baseCondition bkr:cond_none, bkr:cond_wild_type_genotype;
agri:log2FoldChange ?fc;
agri:pvalue ?pvalue;
agri:evidence bkr:exp_E-MTAB-8073;
.
FILTER ( ?pvalue < 0.05 )
FILTER ( ABS( ?fc ) > 1 )
}""", "DEX statements about sodium_chloride not found!")
self.assertTrue(
"wild type genotype" in cond_labels,
"Extended base condition in DEX experiment not found!")