def process_mesh(graph: nx.DiGraph, iri: Optional[str] = None):
"""Process the MeSH NetworkX graph."""
import owlready
assert nx.is_directed_acyclic_graph(graph)
o = owlready.Ontology(iri if iri is not None else MESH_OWL_IRI)
kwd = {"ontology": o}
node_cls = {
ROOT_NAME: types.new_class(ROOT_NAME, (owlready.Thing, ), kwds=kwd)
}
def recur(pnode):
for neighbor in graph.successors(pnode):
if neighbor not in node_cls:
node_cls[neighbor] = types.new_class(neighbor,
(node_cls[pnode], ),
kwds=kwd)
owlready.ANNOTATIONS[node_cls[neighbor]].add_annotation(
owlready.rdfs.label, graph.node[pnode]['label'])
recur(neighbor)
recur(ROOT_NAME)
return o
def nx_to_ontology(graph, source_node, output_path, base_iri):
"""Graph nodes are ID's, and have a 'label' in the node data with the right label
:param graph:
:param source_node:
:param str output_path:
:param base_iri:
"""
ontology = owlready.Ontology(base_iri)
parent_lookup = {
source_node:
types.new_class(source_node, (owlready.Thing, ),
kwds={"ontology": ontology})
}
def recur(pnode):
for neighbor in graph.neighbors(pnode):
data = graph.node[neighbor]
neighbor_class = types.new_class(neighbor,
(parent_lookup[pnode], ),
kwds={"ontology": ontology})
owlready.ANNOTATIONS[neighbor_class].add_annotation(
owlready.rdfs.label, data['label'])
recur(neighbor)
recur(source_node)
ontology.save(filename=output_path)
import owlready as owr
import os
owr.onto_path.append(os.getcwd())
onto = owr.Ontology("http://pyonto.com/ontologies/pyonto.owl")
class Drug(owr.Thing):
ontology = onto
class DrugAssociation(Drug):
pass
class has_for_cost(owr.FunctionalProperty):
ontology = onto
domain = [Drug]
range = [float]
onto.save()
Translation.find_binary_predicates(a[0], binary_predicates)
print('-----------')
#pp.pprint(s)
print('')
#print(is_all_unary(translated[1]))
#pp.pprint(translated)
print(unary_predicates)
print(binary_predicates)
for u in unary_predicates:
unary.add(u[0])
for b in binary_predicates:
binary.add(b[0])
print('=======')
onto = owlready.Ontology("http://1337.io/onto.owl")
classes = {u: owl_class(u, onto) for u in unary}
properties = {owl_property(b, onto) for b in binary}
print(onto.classes)
print(onto.properties)
print('=======')
print(owlready.to_owl(onto))