def _populate_published(curation_export, graphs):
# datasets = [list(g[:rdf.type:sparc.Dataset]) for g in graphs]
published_graphs = [
g for g, doi in [(g, list(g[ds:TEMP.hasDoi])) for g in graphs
for ds in g[:rdf.type:sparc.Dataset]] if doi
]
merged = OntGraph()
for g in published_graphs:
merged.namespace_manager.populate_from({
k: v
for k, v in dict(g.namespace_manager).items()
if k not in ('contributor', 'sample', 'subject')
})
merged.populate_from_triples(
g.data) # g.data excludes the owl:Ontology section
# TODO switch the rdf:type of metadata section on combination to preserve export related metadata
mg = curation_export.metadata().graph
mg.namespace_manager.populate(merged)
new_bi = rdflib.URIRef(
mg.boundIdentifier.replace('ontologies/', 'ontologies/published/'))
new_vi = rdflib.URIRef(
mg.versionIdentifier.replace('ontologies/', 'ontologies/published/'))
replace_pairs = (
(rdflib.Literal("SPARC Consortium curation export published graph"),
rdflib.Literal("SPARC Consortium curation export graph")),
(new_bi, mg.boundIdentifier), (new_vi, mg.versionIdentifier))
new_meta = mg.replaceIdentifiers(replace_pairs)
new_meta.populate(merged)
return merged
def main():
olr = auth.get_path('ontology-local-repo')
ori = OntResIri('http://purl.obolibrary.org/obo/doid.owl')
orp = OntResPath(olr / 'ttl/external/doid.owl')
ort = ori
g = ori.graph
query = """
SELECT DISTINCT ?s ?o ?l
WHERE {
?s a owl:Class .
?s rdfs:subClassOf* <http://purl.obolibrary.org/obo/DOID_4> .
?s rdfs:subClassOf ?o .
?s rdfs:label ?l .
}"""
res = list(g.query(query))
filt = [r for r in res if not isinstance(r[1], rdflib.BNode)]
spath = 'ttl/generated/doidslim.ttl'
go = OntGraph(path=olr / spath)
# TODO prov record like the one we have for chebi
go.bind('DOID', 'http://purl.obolibrary.org/obo/DOID_')
s = rdflib.URIRef('http://ontology.neuinfo.org/NIF/' + spath)
go.populate_from_triples(
((s, p, o) for p, o in
((rdf.type, owl.Ontology),
(rdfs.label, rdflib.Literal("NIF DOID slim")),)))
ds = rdflib.URIRef('http://purl.obolibrary.org/obo/DOID_4')
go.add((ds, rdf.type, owl.Class))
go.add((ds, rdfs.label, rdflib.Literal('disease')))
go.populate_from_triples(
(t for s, o, l in filt for t in
((s, rdf.type, owl.Class),
(s, rdfs.subClassOf, o),
(s, rdfs.label, l))))
go.write()
def make_graphs(g, pids, published):
sgs = []
for i in pids:
ng = OntGraph()
ng.namespace_manager.populate_from(g)
ng.namespace_manager.bind(
'spjl', 'https://uilx.org/tgbugs/u/sparcur-protcur-json-ld/')
ng.populate_from_triples(tobn(g.subjectGraphClosure(i), published))
sgs.append(ng)
return sgs
def main():
url = (
'http://data.bioontology.org/ontologies/'
f'PCL/submissions/7/download?apikey={auth.user_config.secrets("bioportal")}'
)
g = OntGraph().parse(url, format='application/rdf+xml')
g = fixns(g)
og = OntGraph()
g.namespace_manager.populate(og)
og.populate_from_triples(to_ebm(g))
og.write('/tmp/pCL.ttl')
def substitute_graph(graph, base_graph=None):
# command triples
# random literals
# random urirefs
g = OntGraph(namespace_manager=base_graph)
trips = [[mkrand(e) for e in t]
for t in graph
if '__COMMAND' not in t[0]]
g.populate_from_triples(trips)
if base_graph is not None:
cmd_trips = [[mkrand(e) for e in t]
for t_command in graph
if '__COMMAND' in t_command[0]
for t in process_command(t_command, base_graph)]
g.populate_from_triples(cmd_trips)
return g
def fixns(g):
ns = rdflib.Namespace(dict(g.namespace_manager)[''])
nsb = ns + 'pCL_'
nsu = ns + 'UBERON_'
nsc = ns + 'CL_'
ng = OntGraph()
ng.namespace_manager.populate_from(g)
ng.bind('ilxtr', ilxtr)
ng.bind('CL', CL)
ng.bind('pCL', pCL)
ng.bind('UBERON', UBERON)
ng.bind('NCBITaxon', NCBITaxon)
ng.bind('HGNC', HGNC)
ng.bind('LOC', LOC)
ng.populate_from_triples(
(rdflib.URIRef(str(e.replace(nsb, pCL))) if e.startswith(nsb) else
(rdflib.URIRef(str(e.replace(nsu, UBERON))) if e.startswith(nsu) else
(rdflib.URIRef(str(e.replace(nsc, CL))) if e.startswith(nsc) else e))
for e in t) for t in g)
return ng
