def testIter(self):
"""PR 1382: adds __iter__ to Dataset"""
d = Dataset()
uri_a = URIRef("https://example.com/a")
uri_b = URIRef("https://example.com/b")
uri_c = URIRef("https://example.com/c")
uri_d = URIRef("https://example.com/d")
d.add_graph(URIRef("https://example.com/g1"))
d.add((uri_a, uri_b, uri_c, URIRef("https://example.com/g1")))
d.add((uri_a, uri_b, uri_c, URIRef("https://example.com/g1")
)) # pointless addition: duplicates above
d.add_graph(URIRef("https://example.com/g2"))
d.add((uri_a, uri_b, uri_c, URIRef("https://example.com/g2")))
d.add((uri_a, uri_b, uri_d,
URIRef("https://example.com/g1"))) # new, uri_d
# traditional iterator
i_trad = 0
for t in d.quads((None, None, None)):
i_trad += 1
# new Dataset.__iter__ iterator
i_new = 0
for t in d:
i_new += 1
self.assertEqual(i_new, i_trad) # both should be 3
def createNanopubs(g):
ds = Dataset()
ds.namespace_manager.bind("ddi","http://purl.org/net/nlprepository/spl-ddi-annotation-poc#")
ds.namespace_manager.bind("prov","http://www.w3.org/ns/prov#")
ds.namespace_manager.bind("np", "http://www.nanopub.org/nschema#")
bindings = g.query(interactSelect)
for b in bindings:
npURI = URIRef(b['inter'] + "-nanopub")
headURI = URIRef(b['inter'] + "-head")
aURI = URIRef(b['inter'] + "-assertion")
pubInfoURI = URIRef(b['inter'] + "-pubInfo")
provURI = URIRef(b['inter'] + "-provenance")
head = ds.add_graph(headURI)
head.add((npURI, RDF.type, np['Nanopublication']))
head.add((aURI, RDF.type, np['Assertion']))
head.add((provURI, RDF.type, np['Provenance']))
head.add((pubInfoURI, RDF.type, np['PublicationInfo']))
head.add((npURI, np['hasAssertion'], aURI))
head.add((npURI, np['hasProvenance'], provURI))
head.add((npURI, np['hasPublicationInfo'], pubInfoURI))
#print head.serialize()
a = ds.add_graph(aURI)
a.add((b['s'], URIRef('http://dbmi-icode-01.dbmi.pitt.edu/dikb/vocab/interactsWith'), b['o']))
a.add((b['s'], RDF.type, sio["SIO_010038"]))
a.add((b['o'], RDF.type, sio["SIO_010038"]))
prov = ds.add_graph(provURI)
prov.add((aURI, w3prov['wasDerivedFrom'], b['inter']))
print ds.serialize(format='trig')
def from_csvw(metadata_filepath):
pmd_metadata = Dataset()
with open(metadata_filepath) as file:
json_string = file.read()
g = Graph().parse(data=json_string, format='json-ld')
# Get all datacubes.
datacubes = g.query("""
PREFIX dcat: <http://www.w3.org/ns/dcat#>
SELECT *
WHERE {
?dataset a dcat:Dataset .
}
""")
for datacube in datacubes:
# Try and find a sensible id for each dcat:Dataset specifed in the
# metadata file to derive additional URIs for PMD resources
datacube_uri = datacube[0]
datacube_id = urlparse(datacube_uri).path.rsplit('/', 1)[-1]
# Create sensible URIs for PMD specific resources
catalog_uri = "http://gss-data.org.uk/catalog/datasets"
graph_uri = f"http://gss-data.org.uk/graph/{datacube_id}"
metadata_graph_uri = f"http://gss-data.org.uk/graph/{datacube_id}#metadata"
catalog_record_uri = f"http://gss-data.org.uk/catalog/{datacube_id}"
dataset_uri = f"http://gss-data.org.uk/data/{datacube_id}"
metadata = Graph('IOMemory', URIRef(metadata_graph_uri))
metadata.bind('dcat', DCAT)
metadata.bind('dct', DCTERMS)
metadata.bind('foaf', FOAF)
metadata.bind('qb', QB)
metadata.bind('pmdcat', PMDCAT)
metadata.bind('rdf', RDF)
metadata.bind('rdfs', RDFS)
metadata.bind('vcard', VCARD)
graph = URIRef(graph_uri)
metadata_graph = URIRef(metadata_graph_uri)
catalog = URIRef(catalog_uri)
catalog_record = URIRef(catalog_record_uri)
dataset = URIRef(dataset_uri)
datacube = URIRef(datacube_uri)
triples = [
# Metadata required by PMD: ------------------------------------
(catalog, RDF.type, DCAT.Catalog),
(catalog, DCAT.record, catalog_record),
(catalog_record, RDF.type, DCAT.CatalogRecord),
(catalog_record, FOAF.primaryTopic, dataset),
(catalog_record, PMDCAT.metadataGraph, metadata_graph),
(dataset, RDF.type, PMDCAT.Dataset),
(dataset, PMDCAT.datasetContents, datacube),
(dataset, PMDCAT.graph, graph),
(datacube, RDF.type, PMDCAT.DataCube)
]
# Get metadata attached to a datacube-like object and assign it
# to the dcat:Dataset catalog entry.
user_defined_metadata = g.query("""
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX csvw: <http://www.w3.org/ns/csvw#>
PREFIX qb: <http://purl.org/linked-data/cube#>
PREFIX vcard: <http://www.w3.org/2006/vcard/ns#>
SELECT ?dataset ?p ?o
WHERE {
{
?datacube ?p ?o .
FILTER (?p NOT IN (
rdf:type, qb:structure, csvw:tableSchema, csvw:url
)) .
}
}
""",
initBindings={
"dataset": dataset,
"datacube": datacube
})
contact_metadata = g.query("""
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX vcard: <http://www.w3.org/2006/vcard/ns#>
SELECT ?contact ?p ?o
WHERE {
{
?datacube ?p0 ?contact .
?contact a vcard:Individual .
?contact ?p ?o .
}
}
""",
initBindings={"datacube": datacube})
triples.extend(list(user_defined_metadata))
triples.extend(list(contact_metadata))
for triple in triples:
if triple[2] is not None:
metadata.add(triple)
pmd_metadata.add_graph(metadata)
pmd_metadata.serialize(metadata_filepath.replace(
".csv-metadata.json", ".trig"),
format="trig")
def createNanopubs(g):
ds = Dataset()
ds.namespace_manager.bind("ddi","http://dbmi-icode-01.dbmi.pitt.edu/mp/")
ds.namespace_manager.bind("np", "http://www.nanopub.org/nschema#")
ds.namespace_manager.bind("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#")
ds.namespace_manager.bind("rdfs", "http://www.w3.org/2000/01/rdf-schema#")
ds.namespace_manager.bind("owl", "http://www.w3.org/2002/07/owl#")
ds.namespace_manager.bind("obo", "http://purl.obolibrary.org/obo/")
ds.namespace_manager.bind("oboInOwl", "http://www.geneontology.org/formats/oboInOwl#")
ds.namespace_manager.bind("xsd", "http://www.w3.org/2001/XMLSchema#")
ds.namespace_manager.bind("dc", "http://purl.org/dc/elements/1.1/")
ds.namespace_manager.bind("mp", "http://purl.org/mp/")
assertionCount = 1
enzymeCount = 1
pddiD = dict([line.split(',',1) for line in open('../../data/np-graphs/processed-dikb-ddis-for-nanopub.csv')])
cL = dict([line.split('\t') for line in open('../../data/chebi_mapping.txt')])
pL = dict([line.split('\t') for line in open('../../data/pro_mapping.txt')])
substrateD = {}
inhibitorD = {}
bindings = g.query(interactSelect)
for b in bindings:
if( pddiD.has_key(str(b['c'].decode('utf-8'))) ):
tempClaim = pddiD[ str(b['c'].decode('utf-8')) ]
claimInfo = tempClaim.split(',')
claimSub = claimInfo[1]
claimObj = claimInfo[2]
predicateType = claimInfo[0].strip('\n')
if(predicateType == "increases_auc"):
aURI = URIRef("http://dbmi-icode-01.dbmi.pitt.edu/mp/ddi-spl-annotation-np-assertion-%s") % assertionCount
assertionCount += 1
bn1 = BNode('1')
bn2 = BNode('2')
bn3 = BNode('3')
bn4 = BNode('4')
bn5 = BNode('5')
bn6 = BNode('6')
bn7 = BNode('7')
bn8 = BNode('8')
bn9 = BNode('9')
bn10 = BNode('10')
assertionLabel = cL[claimSub.strip('\n')].strip('\n') + " - " + cL[claimObj.strip('\n')].strip('\n') + " potential drug-drug interaction"
a = ds.add_graph((aURI))
a.add(( aURI, RDF.type, np.assertion))
a.add(( aURI, RDF.type, owl.Class))
a.add(( aURI, RDFS.label, (Literal(assertionLabel.lower()))))
a.add(( aURI, RDFS.subClassOf, URIRef("http://purl.obolibrary.org/obo/DIDEO_00000000")))
a.add(( bn1, RDF.type, owl.Restriction))
a.add(( bn1, owl.onProperty, URIRef("http://purl.obolibrary.org/obo/IAO_0000136")))
a.add(( bn2, RDF.type, owl.Class))
a.add(( bn3, RDF.first, URIRef("http://purl.obolibrary.org/obo/DIDEO_00000012")))
a.add(( bn5, RDF.first, bn4))
a.add(( bn3, RDF.rest, bn5))
a.add(( bn4, RDF.type, owl.Restriction))
a.add(( bn4, owl.onProperty, URIRef("http://purl.obolibrary.org/obo/BFO_0000052")))
a.add(( bn4, owl.hasValue, URIRef(claimSub.strip('\n'))))
a.add(( bn5, RDF.rest, RDF.nil))
a.add(( bn2, owl.intersectionOf, bn3))
a.add(( bn1, owl.someValuesFrom, bn2))
a.add(( aURI, RDFS.subClassOf, bn1))
a.add(( bn6, RDF.type, owl.Restriction))
a.add(( bn6, owl.onProperty, URIRef("http://purl.obolibrary.org/obo/IAO_0000136")))
a.add(( bn7, RDF.type, owl.Class))
a.add(( bn8, RDF.first, URIRef("http://purl.obolibrary.org/obo/DIDEO_00000013")))
a.add(( bn10, RDF.first, bn9))
a.add(( bn8, RDF.rest, bn10))
a.add(( bn9, RDF.type, owl.Restriction))
a.add(( bn9, owl.onProperty, URIRef("http://purl.obolibrary.org/obo/BFO_0000052")))
a.add(( bn9, owl.hasValue, URIRef(claimObj.strip('\n'))))
a.add(( bn10, RDF.rest, RDF.nil))
a.add(( bn7, owl.intersectionOf, bn8))
a.add(( bn6, owl.someValuesFrom, bn7))
a.add(( aURI, RDFS.subClassOf, bn6))
ds.add(( aURI, mp.formalizes, b['c']))
ds.add(( b['c'], mp.formalizedAs, aURI))
elif(predicateType == "substrate_of"):
aURI = URIRef("http://dbmi-icode-01.dbmi.pitt.edu/mp/ddi-spl-annotation-np-assertion-%s") % assertionCount
assertionCount += 1
dLabel = cL[claimSub.strip('\n')].strip('\n')
eLabel = pL[claimObj.strip('\n')].strip('\n')
assertionLabel = dLabel + " substrate of " + eLabel
a = ds.add_graph((aURI))
ds.add(( aURI, RDF.type, np.assertion))
ds.add(( aURI, RDFS.label, Literal(assertionLabel.lower())))
ds.add(( aURI, mp.formalizes, b['c']))
ds.add(( b['c'], mp.formalizedAs, aURI))
a.add(( URIRef(claimObj.strip('\n')), RDF.type, URIRef("http://purl.obolibrary.org/obo/OBI_0000427")))
a.add(( URIRef(claimObj.strip('\n')), RDFS.label, Literal(eLabel.lower())))
a.add(( URIRef(claimObj.strip('\n')), URIRef("http://purl.obolibrary.org/obo/DIDEO_00000096"), URIRef(claimSub.strip('\n'))))
a.add(( URIRef(claimSub.strip('\n')), RDF.type, URIRef("http://purl.obolibrary.org/obo/CHEBI_24431")))
a.add(( URIRef(claimSub.strip('\n')), RDFS.label, Literal(dLabel.lower())))
elif(predicateType == "inhibits"):
aURI = URIRef("http://dbmi-icode-01.dbmi.pitt.edu/mp/ddi-spl-annotation-np-assertion-%s") % assertionCount
assertionCount += 1
dLabel = cL[claimSub.strip('\n')].strip('\n')
eLabel = pL[claimObj.strip('\n')].strip('\n')
assertionLabel = dLabel + " inhibits " + eLabel
a = ds.add_graph((aURI))
ds.add(( aURI, RDF.type, np.assertion))
ds.add(( aURI, RDFS.label, Literal(assertionLabel.lower())))
ds.add(( aURI, mp.formalizes, b['c']))
ds.add(( b['c'], mp.formalizedAs, aURI))
a.add(( URIRef(claimSub.strip('\n')), RDF.type, URIRef("http://purl.obolibrary.org/obo/CHEBI_24431")))
a.add(( URIRef(claimSub.strip('\n')), RDFS.label, Literal(dLabel.lower())))
a.add(( URIRef(claimSub.strip('\n')), URIRef("http://purl.obolibrary.org/obo/RO_0002449"), URIRef(claimObj.strip('\n'))))
print ds.serialize(format='trig')
def createNanopubs(g):
ds = Dataset()
ds.namespace_manager.bind("ddi","http://dbmi-icode-01.dbmi.pitt.edu/mp/")
ds.namespace_manager.bind("np", "http://www.nanopub.org/nschema#")
ds.namespace_manager.bind("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#")
ds.namespace_manager.bind("rdfs", "http://www.w3.org/2000/01/rdf-schema#")
ds.namespace_manager.bind("owl", "http://www.w3.org/2002/07/owl#")
ds.namespace_manager.bind("obo", "http://purl.obolibrary.org/obo/")
ds.namespace_manager.bind("oboInOwl", "http://www.geneontology.org/formats/oboInOwl#")
ds.namespace_manager.bind("xsd", "http://www.w3.org/2001/XMLSchema#")
ds.namespace_manager.bind("dc", "http://purl.org/dc/elements/1.1/")
ds.namespace_manager.bind("mp", "http://purl.org/mp/")
ds.namespace_manager.bind("prov", "http://www.w3.org/ns/prov#")
ds.namespace_manager.bind("dikbEvidence", "http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/DIKB_evidence_ontology_v1.3.owl#")
bindings = g.query(interactSelect)
for b in bindings:
asIndex = b['a'].decode('utf-8').rfind('-')
identifier = b['a'].decode('utf-8')[asIndex:]
predicateType = b['t'].decode('utf-8')
npURI = URIRef('http://dbmi-icode-01.dbmi.pitt.edu/mp/ddi-spl-annotation-nanopub%s') % identifier
headURI = URIRef('http://dbmi-icode-01.dbmi.pitt.edu/mp/ddi-spl-annotation-np-head%s') % identifier
pubInfoURI = URIRef('http://dbmi-icode-01.dbmi.pitt.edu/mp/ddi-spl-annotation-np-pubInfo%s') % identifier
provURI = URIRef('http://dbmi-icode-01.dbmi.pitt.edu/mp/ddi-spl-annotation-np-provenance%s') % identifier
aURI = URIRef('http://dbmi-icode-01.dbmi.pitt.edu/mp/ddi-spl-annotation-np-assertion%s') % identifier
ds.add(( aURI, RDF.type, np.assertion))
head = ds.add_graph(headURI)
head.add((npURI, RDF.type, np['Nanopublication']))
head.add((provURI, RDF.type, np['Provenance']))
head.add((pubInfoURI, RDF.type, np['PublicationInfo']))
head.add((npURI, np['hasAssertion'], aURI))
head.add((npURI, np['hasProvenance'], provURI))
head.add((npURI, np['hasPublicationInfo'], pubInfoURI))
pub = ds.add_graph(pubInfoURI)
pub.add((npURI, prov.wasAttributedTo, URIRef('http://orcid.org/0000-0002-2993-2085')))
pub.add((npURI, prov.generatedAtTime, Literal(datetime.now()) ))
if(predicateType == "http://purl.obolibrary.org/obo/DIDEO_00000000"):
provenance = ds.add_graph(provURI)
provenance.add(( aURI, prov.wasAttributedTo, URIRef('http://orcid.org/0000-0002-2993-2085')))
provenance.add(( aURI, prov.generatedAtTime, Literal(datetime.now()) ))
provenance.add(( aURI, prov.wasDerivedFrom, Literal("Derived from the DIKB's evidence base using the listed belief criteria")))
provenance.add(( aURI, prov.hadMember, dikbEvidence.EV_PK_DDI_RCT ))
provenance.add(( aURI, prov.hadMember, dikbEvidence.EV_PK_DDI_NR ))
provenance.add(( aURI, prov.hadMember, dikbEvidence.EV_PK_DDI_Par_Grps ))
elif(predicateType == "http://purl.obolibrary.org/obo/DIDEO_00000096"):
provenance = ds.add_graph(provURI)
provenance.add(( aURI, prov.wasAttributedTo, URIRef('http://orcid.org/0000-0002-2993-2085')))
provenance.add(( aURI, prov.generatedAtTime, Literal(datetime.now()) ))
provenance.add(( aURI, prov.wasDerivedFrom, Literal("Derived from the DIKB's evidence base using the listed belief criteria")))
provenance.add(( aURI, prov.hadMember, dikbEvidence.EV_PK_DDI_RCT ))
provenance.add(( aURI, prov.hadMember, dikbEvidence.EV_PK_DDI_NR ))
provenance.add(( aURI, prov.hadMember, dikbEvidence.EV_PK_DDI_Par_Grps ))
provenance.add(( aURI, prov.hadMember, dikbEvidence.EV_CT_PK_Genotype ))
provenance.add(( aURI, prov.hadMember, dikbEvidence.EV_CT_PK_Phenotype ))
elif(predicateType == "http://purl.obolibrary.org/obo/RO_0002449"):
provenance = ds.add_graph(provURI)
provenance.add(( aURI, prov.wasAttributedTo, URIRef('http://orcid.org/0000-0002-2993-2085')))
provenance.add(( aURI, prov.generatedAtTime, Literal(datetime.now()) ))
provenance.add(( aURI, prov.wasDerivedFrom, Literal("Derived from the DIKB's evidence base using the listed belief criteria")))
provenance.add(( aURI, prov.hadMember, dikbEvidence.EV_PK_DDI_RCT ))
provenance.add(( aURI, prov.hadMember, dikbEvidence.EV_PK_DDI_NR ))
provenance.add(( aURI, prov.hadMember, dikbEvidence.EV_PK_DDI_Par_Grps ))
print ds.serialize(format='trig')
