Examples from the lectures

From Info216

This page contains code examples from the lectures.

S02

Getting started with RDFlib

from inspect import formatargspec
from rdflib import Graph, Literal, RDF, FOAF, Namespace

g = Graph()

EX = Namespace('http://ex.org/')

g.add((EX.Bob, RDF.type, FOAF.Person))
g.add((EX.Alice, RDF.type, FOAF.Person))
g.add((EX.Carol, RDF.type, FOAF.Person))
g.add((EX.Bob, FOAF.knows, EX.Alice))
g.add((EX.Bob, FOAF.knows, EX.Carol))

g.add((EX.Bob, FOAF.name, Literal('Bob')))
g.add((EX.Alice, FOAF.name, Literal('Alice')))
g.add((EX.Carol, FOAF.name, Literal('Carol')))

g.namespace_manager.bind('ex', EX)

print(g.serialize(format='json-ld'))

for p, o in g[ EX.Bob : : ]:
    print(p, o)


g2 = Graph()
g2.parse('https://www.wikidata.org/entity/Q935079.ttl')
print(g2.serialize())

S03

Local query with RDFlib

from rdflib import Graph, Namespace

REX = Namespace('http://example.org/royal#')

g = Graph()
g.parse('family.ttl', format='ttl')
res = g.query("""
    CONSTRUCT {
        ?child fam:aunt ?aunt .
    } WHERE {
        ?child fam:hasParent / fam:hasSister ?aunt .
    }
""",
    initNs={
        'fam': 'http://example.org/family#'
    },
    initBindings={
        'child': REX.SverreMagnus
    })

S04

Remote query with SPARQLWrapper

import SPARQLWrapper

endpoint = 'http://sandbox.i2s.uib.no/bigdata/namespace/kb/sparql'

paper_uri = 'http://semanticscholar.org/paper/c93a37e6922e09f34fc093f7e4f9675775d4557d'

client = SPARQLWrapper.SPARQLWrapper(endpoint=endpoint)
client.setReturnFormat('json')
client.setQuery(f'''
    DESCRIBE <{paper_uri}>
''')
res = client.queryAndConvert()

Remote update with SPARQLWrapper

client.setReturnFormat('xml')
client.setMethod('POST')
client.setQuery('''
    DELETE DATA {
        <http://example.org/Abra> <http://example.org/ka> <http://example.org/Dabra> .
    }
''')
res = client.queryAndConvert()
client.setMethod('GET')

Local update with RDFlib

from rdflib import Graph, Namespace

g = Graph()
g.parse('family.ttl', format='turtle')

FAM = Namespace('http://example.org/family#')
g.update('''
    DELETE {
        ?child fam:hasAunt ?parent .
    } INSERT {
        ?child fam:hasAunt ?sister .
    } WHERE {
        ?child fam:hasParent ?parent .
        ?parent fam:hasSister ?sister .
    }
    ''',
    initNs={
        'fam': FAM
    })

print(g.serialize(format='turtle'))

S07

RDFS programming with owlrl .

Syllogism (rule rdfs9)

from rdflib import Graph, RDF, RDFS, OWL, Namespace
import owlrl

EX = Namespace('http://example.org#')

g = Graph()
g.bind('', EX)
NS = {
    '': EX,
    'rdf': RDF,
    'rdfs': RDFS,
}
g.update("""
INSERT DATA {
    :Socrates rdf:type :Man .
    :Man rdfs:subClassOf :Mortal .
}
""", initNs=NS)

rdfs_engine = owlrl.RDFSClosure.RDFS_Semantics(g, True, False, False)
rdfs_engine.closure()
rdfs_engine.flush_stored_triples()

res = g.query("""
ASK { :Socrates rdf:type :Mortal . }
""", initNs=NS)
print(res.askAnswer)

Domain and range (rules rdfs2-3)

from rdflib import Graph, RDF, RDFS, OWL, Namespace
import owlrl

EX = Namespace('http://example.org#')

g = Graph()
g.bind('', EX)
NS = {
    '': EX,
    'rdf': RDF,
    'rdfs': RDFS,
}
g.update("""
INSERT DATA {
    :Socrates :husbandOf :Xantippe .
    :husbandOf rdfs:domain :Man .
    :husbandOf rdfs:range :Woman .
}
""", initNs=NS)

rdfs_engine = owlrl.RDFSClosure.RDFS_Semantics(g, True, False, False)
rdfs_engine.closure()
rdfs_engine.flush_stored_triples()

res = g.query("""
ASK { :Xantippe rdf:type :Woman . }
""", initNs=NS)
print(res.askAnswer)

S08

owl:inverseOf

from rdflib import Graph, Namespace, RDF, RDFS, FOAF
import owlrl


EX = Namespace('http://ex.org/')

g = Graph()
g.bind('', EX)
g.add((EX.Andreas, RDF.type, EX.Teacher))
g.add((EX.Martin, RDF.type, EX.Teacher))
g.add((EX.Tobias, RDF.type, EX.Teacher))
g.add((EX.Martin, RDF.type, EX.Student))
g.add((EX.Tobias, RDF.type, EX.Student))
g.add((EX.Mariah, RDF.type, EX.Student))
g.add((EX.Bahareh, RDF.type, EX.Student))
# g.add((EX.Teacher, RDFS.subClassOf, FOAF.Person))
# g.add((EX.Student, RDFS.subClassOf, FOAF.Person))


g.update("""
INSERT DATA {
    :Martin :hasSupervisor :Andreas .
    :hasSupervisor owl:inverseOf :supervisorOf .
}
""")

This gives no response:

res = g.query("""
SELECT ?person WHERE {
    :Andreas :supervisorOf ?person .
}
""")
print(res.serialize(format='txt').decode())

Not this either:

engine = owlrl.CombinedClosure.RDFS_OWLRL_Semantics(g, False, False, False)
engine.closure()
engine.flush_stored_triples()

res = g.query("""
SELECT ?person WHERE {
    :Andreas :supervisorOf ?person .
}
""")
print(res.serialize(format='txt').decode())

But this prints out a response:

engine = owlrl.CombinedClosure.RDFS_OWLRL_Semantics(g, False, False, False)
engine.closure()
engine.flush_stored_triples()

res = g.query("""
SELECT ?person WHERE {
    :Andreas :supervisorOf ?person .
}
""")
print(res.serialize(format='txt').decode())

S11

Simple DL reasoning in Protégé

Download the OWL file, and remove the ".txt" suffix (required by the wiki platform).

Load the renamed file into Protege-OWL. From the "Reasoner" menu, choose "HermiT ..." and then "Start reasoner" to see the results of reasoning. Whenever you change the ontology, use "Synchronize reasoner" to update the reasoning results.

Simple DL reasoning in Python's owlready2

First you need to

   pip install owlready2

then you can run this:

import os 

from owlready2 import *


# on Windows, the HermiT reasoner needs to find Java
TEMP_DIR = 'temp_owlready2/'
if os.name=='nt':
    JAVA_EXE = 'C:\\Program Files\\Java\\jre1.8.0_251'
    # JAVA_EXE = os.getenv('JRE_HOME')

# load the ontology we have saved from Protege-OWL (save in RDF-XML or OWL-XML format)
EX = 'file://ex-prop-res.owl'
onto = get_ontology(EX)
onto.load('file://ex-prop-res.owl')

# pick out all the triples inside owlready2 as an rdflib Graph 
g = default_world.as_rdflib_graph()
print(g.serialize(format='ttl'))

# use an owlready2 method to loop through all the individuals in the ontology
for ind in onto.individuals():
    print(ind, ind.is_a)

# run the built-in HermiT reasoner
sync_reasoner()

# loop through the individuals again to see the new types added by HermiT
for ind in onto.individuals():
    print(ind, ind.is_a)

Simple ontology creation in Python's owlready2

The code below does the same thing, but instead of reading the ontology from a file, it defines it using owlready2:

import os 

from owlready2 import *


TEMP_DIR = 'temp_owlready2/'
if os.name=='nt':
    JAVA_EXE = 'C:\\Program Files\\Java\\jre1.8.0_251'
    # JAVA_EXE = os.getenv('JRE_HOME')

EX = 'http://info216.uib.no/ex-prop-res/'
onto = get_ontology(EX)

# get_ontology(EX) will reload the ontology if it already exists in your workspace, 
# so we need to empty it
for ind in onto.individuals():
    destroy_entity(ind)
for cls in onto.classes():
    destroy_entity(cls)

with onto:
    # add classes, properties and individuals to the 'onto' ontology
    class Person(Thing): pass
    class Woman(Person): pass
    class hasSibling(SymmetricProperty): 
        domain = [Person]
        range = [Person]

    marthaLouise = Woman('MarthaLouise')
    ingridAlexandra = Woman('IngridAlexandra')
    haakonMagnus = Person('HaakonMagnus')
    sverreMagnus = Person('SverreMagnus')

    haakonMagnus.hasSibling = [marthaLouise]
    ingridAlexandra.hasSibling = [sverreMagnus]

# have a look at the triples in Turtle
g = default_world.as_rdflib_graph()
print(g.serialize(format='ttl'))

Add the restriction classes too:

with onto:
    class Sister(Person):
        equivalent_to = [Woman & hasSibling.some(Thing)]

    class Parent(Person): pass
    class Aunt(Person):
        equivalent_to = [Sister & hasSibling.some(Parent)]

    marthaLouise.is_a.append(Parent)
    haakonMagnus.is_a.append(Parent)

Now you can look at the turtle again, and list all the individuals and their types (classes):

g = default_world.as_rdflib_graph()
print(g.serialize(format='ttl'))

for ind in onto.individuals():
    print(ind, ind.is_a)

Run the reasoner:

sync_reasoner()

List the individuals and their types again to see (some of) the results of reasoning.