def declare_individual(self, entity_id):
entity = genid(base=self.writer.writer.base + '/')
# TODO: Make this add_to_graph
self.writer.emit_type(entity, self.writer.uri(entity_id))
self.writer.emit_type(entity, OWL.NamedIndividual)
self.individuals[entity_id] = entity
return entity
def find_or_create_evidence_id(self, evidence):
for existing_evidence in self.evidences:
if evidence.evidence_code == existing_evidence.evidence_code and set(evidence.references) == set(existing_evidence.references):
if existing_evidence.id is None:
existing_evidence.id = genid(base=self.writer.base + '/')
self.ev_ids.append(existing_evidence.id)
return existing_evidence.id
return self.create_evidence(evidence)
def add_individual(self, individual_id, annoton):
obj_uri = self.uri(individual_id)
if individual_id not in annoton.individuals:
tgt_id = genid(base=self.writer.base + '/')
annoton.individuals[individual_id] = tgt_id
self.emit_type(tgt_id, obj_uri)
self.emit_type(tgt_id, OWL.NamedIndividual)
else:
tgt_id = annoton.individuals[individual_id]
def create_evidence(self, evidence):
# Use/figure out standard for creating URIs
# Find minerva code to generate URI, add to Noctua doc
ev_id = genid(base=self.writer.base + '/')
evidence.id = ev_id
# ev_cls = self.eco_class(self.uri(evidence.evidence_code))
# ev_cls = self.eco_class(evidence.evidence_code) # This is already ECO:##### due to a GPAD being used
ev_cls = self.uri(evidence.evidence_code)
self.emit_type(ev_id, OWL.NamedIndividual)
self.emit_type(ev_id, ev_cls)
self.emit(ev_id, DC.date, Literal(evidence.date))
if evidence.with_from:
self.emit(ev_id, URIRef("http://geneontology.org/lego/evidence-with"), Literal(evidence.with_from))
for c in evidence.contributors:
self.emit(ev_id, DC.contributor, Literal(c))
ref_to_emit = ReferencePreference().pick(evidence.references)
o = Literal(ref_to_emit) # Needs to go into Noctua like 'PMID:####' rather than full URL
self.emit(ev_id, HAS_SUPPORTING_REFERENCE, o)
self.evidences.append(evidence)
return evidence.id
def __init__(self, modeltitle, store=None):
self.base = genid(base="http://model.geneontology.org")
if store is not None:
graph = rdflib.Graph(identifier=self.base, store=store)
else:
graph = rdflib.Graph(identifier=self.base)
self.graph = graph
self.graph.bind("owl", OWL)
self.graph.bind("obo", "http://purl.obolibrary.org/obo/")
self.graph.bind("dc", DC)
self.graph.bind("rdfs", RDFS)
self.graph.add((self.base, RDF.type, OWL.Ontology))
# Model attributes TODO: Should move outside init
self.graph.add((self.base, URIRef("http://purl.org/pav/providedBy"), Literal("http://geneontology.org")))
self.graph.add((self.base, DC.date, Literal(str(now.year) + "-" + str(now.month) + "-" + str(now.day))))
self.graph.add((self.base, DC.title, Literal(modeltitle)))
self.graph.add((self.base, DC.contributor, Literal("http://orcid.org/0000-0002-6659-0416"))) #TODO
self.graph.add((self.base, URIRef("http://geneontology.org/lego/modelstate"), Literal("development")))
self.graph.add((self.base, OWL.versionIRI, self.base))