Skip to content

Latest commit

 

History

History
232 lines (191 loc) · 8.3 KB

README.md

File metadata and controls

232 lines (191 loc) · 8.3 KB
Raw

Owl in a bucket

Pyversions PyPi Build Publish

FunOwl - Functional OWL syntax for Python

OWL2 Functional Style Syntax for python.

Goals

To date, it appears that the majority of the python based OWL generators use variations of the OWL RDF syntax -- something that is time consuming and error prone. What we are attempting to do in this project is (in order of relative priority):

  1. Provide a pythonic API that follows the OWL functional model for constructing OWL
  2. Emit OWL in OWL Functional syntax
  3. Emit OWL in RDF (any rdflib flavor)
  4. Consume OWL functional syntax
  5. Consume OWL RDF
  6. Provide a py4j or equivalent wrapper to the standard Java OWL libraries

Goal 1: Create OWL Functional Syntax using Python

from rdflib import RDFS, OWL, Namespace
from funowl import OntologyDocument, Ontology

EX = Namespace("http://www.example.com/ontology1#")

o = Ontology("http://www.example.com/ontology1")
o.imports("http://www.example.com/ontology2")
o.annotation(RDFS.label, "An example")
o.subClassOf(EX.Child, OWL.Thing)
doc = OntologyDocument(EX, o)
print(str(doc))

Output

Prefix( xml: = <http://www.w3.org/XML/1998/namespace> )
Prefix( rdf: = <http://www.w3.org/1999/02/22-rdf-syntax-ns#> )
Prefix( rdfs: = <http://www.w3.org/2000/01/rdf-schema#> )
Prefix( xsd: = <http://www.w3.org/2001/XMLSchema#> )
Prefix( owl: = <http://www.w3.org/2002/07/owl#> )
Prefix( : = <http://www.example.com/ontology1#> )

Ontology( <http://www.example.com/ontology1>
    Import( <http://www.example.com/ontology2> )
    Annotation( rdfs:label "An example" )
    SubClassOf( :Child owl:Thing )
)

Represent:

Prefix(:=<http://example.org/>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Ontology(
  Declaration(NamedIndividual(:a))
  Declaration(DataProperty(:dp))
  Declaration(Class(:A))
  SubClassOf(:A DataAllValuesFrom(:dp 
    DataOneOf("3"^^xsd:integer "4"^^xsd:int))
  ) 
  SubClassOf(:A DataAllValuesFrom(:dp 
    DataOneOf("2"^^xsd:short "3"^^xsd:int))
  )
  ClassAssertion(:A :a)
  ClassAssertion(DataSomeValuesFrom(:dp 
    DataOneOf("3"^^xsd:integer)) :a
  )
)

As:

from rdflib import Namespace, XSD, OWL, Literal
from funowl import *

EX = Namespace("http://example.org/")

# Ontology represents the OWLF OntologyDocument production
o = Ontology(EX.myOntology, "http://example.org/myOntolology/version/0.1")

# prefixes array includes default
o.prefixes(EX, rdfs=RDFS)
o.prefixes.append(owl=OWL)

# namedIndividual, objectProperty, class, et. properties add to declarations
o.namedIndividual(EX.a)

# Declarations can also be added explicitly
o.declarations(DataProperty(EX.dp), Class(EX.A))

# Axioms are added by type
o.subClassOf(EX.A, DataAllValuesFrom(EX.dp, DataOneOf(3, Literal(4, datatype=XSD.int_))))

# or as an array
o.axioms.append(SubClassOf(EX.A, DataAllValuesFrom(EX.dp, DataOneOf(Literal(2, datatype=XSD.short), Literal(3, datatype=XSD.int_))))
o.class(EX.A, EX.a)
o.class(DataSomeValuesFrom(EX.dp, DataOneOf(3)), EX.a)

print(str(o))
Prefix(:=<http://example.org/>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Ontology( 
  Declaration(NamedIndividual(:a))
  Declaration(DataProperty(:dp))
  Declaration(Class(:A))
  SubClassOf(:A DataAllValuesFrom(:dp 
    DataOneOf("3"^^xsd:integer "4"^^xsd:int))
  ) 
  SubClassOf(:A DataAllValuesFrom(:dp 
    DataOneOf("2"^^xsd:short "3"^^xsd:int))
  )
  ClassAssertion(:A :a)
  ClassAssertion(DataSomeValuesFrom(:dp 
    DataOneOf("3"^^xsd:integer)) :a
  )
)

Transforming Functional Syntax to RDF

See: test_issue_57.py for full example

from rdflib import Graph
from funowl.converters.functional_converter import to_python

# The functional syntax input can be a string, URL, file loc or open file
function_pizza = "https://github.com/Harold-Solbrig/funowl/blob/main/tests/data/pizza.owl"
internal_pizza = to_python(function_pizza)

# Emit the internal representation as an rdflib graph
g = Graph()
internal_pizza.to_rdf(g)

# Serialize the rdflib graph in your favorite format
print(g.serialize(format="ttl"))

Command Line Interface

funowl can be installed with either pip or pipenv.

> funowl -h 
usage: funowl [-h]
              [-f {ttl,hext,json-ld,longturtle,n3,nquads,nt,nt11,ntriples,pretty-xml,trig,trix,ttl,turtle,xml}]
              [-np]
              input [output]

Convert OWL Functional Syntax to RDF

positional arguments:
  input                 Input OWL functional syntax. Can be a file name or URL
  output                Output file. If omitted, output goes to stdout

options:
  -h, --help            show this help message and exit
  -f {ttl,hext,json-ld,longturtle,n3,nquads,nt,nt11,ntriples,pretty-xml,trig,trix,ttl,turtle,xml}, --format {ttl,hext,json-ld,longturtle,n3,nquads,nt,nt11,ntriples,pretty-xml,trig,trix,ttl,turtle,xml}
                        Output RDF Format. If omitted, guess from output file
                        suffix. If guessing doesn't work, assume 'turtle'
  -np, --noProgressBar  Don't output the progress indicators

To convert an OWL functional representation of the pizza ontology to RDF:

> funowl https://raw.githubusercontent.com/Harold-Solbrig/funowl/main/tests/data/pizza.owl
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix pizza: <http://www.co-ode.org/ontologies/pizza/pizza.owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix terms: <http://purl.org/dc/terms/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

dc:description a owl:AnnotationProperty .

dc:title a owl:AnnotationProperty .

terms:contributor a owl:AnnotationProperty .

terms:license a owl:AnnotationProperty .

terms:provenance a owl:AnnotationProperty .

<http://www.co-ode.org/ontologies/pizza> a owl:Ontology ;
    rdfs:label "pizza"^^xsd:string ;
    dc:description """An ontology about pizzas and their toppings.
      ...

To convert the same ontology into XML, either:

funowl https://raw.githubusercontent.com/Harold-Solbrig/funowl/main/tests/data/pizza.owl -f xml > pizza.xml

or

funowl https://raw.githubusercontent.com/Harold-Solbrig/funowl/main/tests/data/pizza.owl pizza.xml

> cat pizza.xml
<?xml version="1.0" encoding="utf-8"?>
<rdf:RDF
   xmlns:dc="http://purl.org/dc/elements/1.1/"
   xmlns:owl="http://www.w3.org/2002/07/owl#"
   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
   xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
   xmlns:skos="http://www.w3.org/2004/02/skos/core#"
   xmlns:terms="http://purl.org/dc/terms/"
>
  <rdf:Description rdf:nodeID="Nd1a614092c234a3b90971238bb6550e8">
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
    <owl:onProperty rdf:resource="http://www.co-ode.org/ontologies/pizza/pizza.owl#hasTopping"/>
    <owl:someValuesFrom rdf:resource="http://www.co-ode.org/ontologies/pizza/pizza.owl#TomatoTopping"/>
  </rdf:Description>
      ...
      
</rdf:RDF>

Other packages

While we would be happy to be corrected, to the best of our knowledge there is to be minimal support for OWL in python.

  • OwlReady2 appears to be the closest thing to what we are looking for, but, as described in this paper it creates an ontology-oriented programming API for ontologies, while what we want is much closer to the raw OWL itself. We have also recently discovered
  • The rdflib infixowl actually comes closer to what we've been trying to accomplish and, had we known of its existence before we got started, we may have chosen to build on it instead of starting from scratch.