include RELEASE-VERSION
include version.py
+include htsworkflow/util/schemas/*.turtle
from htsworkflow.submission import daf, ucsc
from htsworkflow.util import api
+from htsworkflow.util.rdfns import *
from htsworkflow.util.rdfhelp import \
- dafTermOntology, \
- dublinCoreNS, \
get_model, \
get_serializer, \
sparql_query, \
submissionOntology, \
libraryOntology, \
- load_into_model, \
- rdfNS, \
- rdfsNS, \
- xsdNS
+ load_into_model
TYPE_N = rdfNS['type']
CREATION_DATE = libraryOntology['date']
from pprint import pprint
from htsworkflow.util.rdfhelp import \
- dafTermOntology, \
- dublinCoreNS, \
get_model, \
get_serializer, \
sparql_query, \
- submissionOntology, \
libraryOntology, \
- load_into_model, \
- rdfNS, \
- rdfsNS, \
- xsdNS
+ load_into_model
+from htsworkflow.util.rdfns import *
TYPE_N = rdfNS['type']
CREATION_DATE = libraryOntology['date']
"""
import collections
from datetime import datetime
+from glob import glob
from urlparse import urlparse, urlunparse
from urllib2 import urlopen
import logging
logger = logging.getLogger(__name__)
-# standard ontology namespaces
-owlNS = RDF.NS('http://www.w3.org/2002/07/owl#')
-dublinCoreNS = RDF.NS("http://purl.org/dc/elements/1.1/")
-rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
-rdfsNS = RDF.NS("http://www.w3.org/2000/01/rdf-schema#")
-xsdNS = RDF.NS("http://www.w3.org/2001/XMLSchema#")
-
-# internal ontologies
-submissionOntology = RDF.NS(
- "http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#")
-dafTermOntology = RDF.NS("http://jumpgate.caltech.edu/wiki/UcscDaf#")
-libraryOntology = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
-inventoryOntology = RDF.NS(
- "http://jumpgate.caltech.edu/wiki/InventoryOntology#")
-submissionLog = RDF.NS("http://jumpgate.caltech.edu/wiki/SubmissionsLog/")
-geoSoftNS = RDF.NS('http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#')
+from htsworkflow.util.rdfns import *
+
+SCHEMAS_URL='http://jumpgate.caltech.edu/phony/schemas'
+INFERENCE_URL='http://jumpgate.caltech.edu/phony/inference'
ISOFORMAT_MS = "%Y-%m-%dT%H:%M:%S.%f"
ISOFORMAT_SHORT = "%Y-%m-%dT%H:%M:%S"
-
def sparql_query(model, query_filename, output_format='text'):
"""Execute sparql query from file
"""
directory = os.getcwd()
if model_name is None:
- storage = RDF.MemoryStorage()
+ storage = RDF.MemoryStorage(options_string="contexts='yes'")
logger.info("Using RDF Memory model")
else:
- options = "hash-type='bdb',dir='{0}'".format(directory)
+ options = "contexts='yes',hash-type='bdb',dir='{0}'".format(directory)
storage = RDF.HashStorage(model_name,
options=options)
logger.info("Using {0} with options {1}".format(model_name, options))
for s in rdf_parser.parse_string_as_stream(data, ns):
conditionally_add_statement(model, s, ns)
+
def fixup_namespace(ns):
if ns is None:
ns = RDF.Uri("http://localhost/")
raise ValueError(errmsg.format(str(type(ns))))
return ns
+
def conditionally_add_statement(model, s, ns):
imports = owlNS['imports']
if s.predicate == imports:
s.object = sanitize_literal(s.object)
model.add_statement(s)
+
+def add_default_schemas(model, schema_path=None):
+ """Add default schemas to a model
+ Looks for turtle files in either htsworkflow/util/schemas
+ or in the list of directories provided in schema_path
+ """
+
+ if schema_path is None:
+ path, _ = os.path.split(__file__)
+ schema_path = [os.path.join(path, 'schemas')]
+ elif type(schema_path) in types.StringTypes:
+ schema_path = [schema_path]
+
+ for p in schema_path:
+ for f in glob(os.path.join(p, '*.turtle')):
+ add_schema(model, f)
+
+def add_schema(model, filename):
+ """Add a schema to a model.
+
+ Main difference from 'load_into_model' is it tags it with
+ a RDFlib context so I can remove them later.
+ """
+ parser = RDF.Parser(name='turtle')
+ context = RDF.Node(RDF.Uri(SCHEMAS_URL))
+ url = 'file://' + filename
+ for s in parser.parse_as_stream(url):
+ try:
+ model.append(s, context)
+ except RDF.RedlandError as e:
+ logger.error("%s with %s", str(e), str(s))
+
+
+def remove_schemas(model):
+ """Remove statements labeled with our schema context"""
+ context = RDF.Node(RDF.Uri(SCHEMAS_URL))
+ model.context_remove_statements(context)
+
+
def sanitize_literal(node):
"""Clean up a literal string
"""
"""
writer = RDF.Serializer(name=name)
# really standard stuff
- writer.set_namespace('owl', owlNS._prefix)
writer.set_namespace('rdf', rdfNS._prefix)
writer.set_namespace('rdfs', rdfsNS._prefix)
+ writer.set_namespace('owl', owlNS._prefix)
+ writer.set_namespace('dc', dcNS._prefix)
+ writer.set_namespace('xml', xmlNS._prefix)
writer.set_namespace('xsd', xsdNS._prefix)
+ writer.set_namespace('vs', vsNS._prefix)
+ writer.set_namespace('wot', wotNS._prefix)
# should these be here, kind of specific to an application
writer.set_namespace('libraryOntology', libraryOntology._prefix)
--- /dev/null
+import RDF
+
+from htsworkflow.util.rdfns import *
+from htsworkflow.util.rdfhelp import SCHEMAS_URL
+
+INFER_URL='http://jumpgate.caltech.edu/phony/infer'
+
+class Infer(object):
+ """Provide some simple inference.
+
+ Provides a few default rules as methods starting with _rule_
+ """
+ def __init__(self, model):
+ self.model = model
+ self._context = RDF.Node(RDF.Uri(INFER_URL))
+
+
+ def update(self, max_iterations=None):
+ """Update model with with inferred statements.
+
+ max_iterations puts a limit on the number of times we
+ run through the loop.
+
+ it will also try to exit if nothing new has been inferred.
+
+ Also this is the naive solution.
+ There's probably better ones out there.
+ """
+ iterations = 0
+ while max_iterations is None or iterations != max_iterations:
+ starting_size = self.model.size()
+
+ for method_name in dir(self):
+ if method_name.startswith('_rule_'):
+ method = getattr(self, method_name)
+ method()
+ if self.model.size() == starting_size:
+ # we didn't add anything new
+ return
+
+ def _rule_inverse_of(self):
+ """Add statements computed with inverseOf
+ """
+ body = """
+ prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+ prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+ prefix owl: <http://www.w3.org/2002/07/owl#>
+
+ select ?o ?reverse ?s
+ where {
+ ?s ?term ?o .
+ ?s a ?subject_type .
+ ?o a ?object_type .
+ ?term owl:inverseOf ?reverse .
+ ?term rdfs:domain ?subject_type ;
+ rdfs:range ?object_type .
+ ?reverse rdfs:domain ?object_type ;
+ rdfs:range ?subject_type .
+ }"""
+ query = RDF.SPARQLQuery(body)
+
+ statements = []
+ for r in query.execute(self.model):
+ s = RDF.Statement(r['o'], r['reverse'], r['s'])
+ if s not in self.model:
+ self.model.append(s, self._context)
+
+
+ def _validate_types(self):
+ body = """
+ prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+ prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+ prefix owl: <http://www.w3.org/2002/07/owl#>
+
+ select ?subject ?predicate ?object
+ where {
+ ?subject ?predicate ?object
+ OPTIONAL { ?subject a ?class }
+ FILTER(!bound(?class))
+ }
+ """
+ query = RDF.SPARQLQuery(body)
+ errmsg = "Missing type for: {0}"
+ for r in query.execute(self.model):
+ yield errmsg.format(str(r['subject']))
+
+ def _validate_undefined_properties(self):
+ """Find properties that aren't defined.
+ """
+ body = """
+ prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+ prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+ prefix owl: <http://www.w3.org/2002/07/owl#>
+
+ select ?subject ?predicate ?object
+ where {
+ ?subject ?predicate ?object
+ OPTIONAL { ?predicate a ?predicate_class }
+ FILTER(!bound(?predicate_class))
+ }"""
+ query = RDF.SPARQLQuery(body)
+ msg = "Undefined property in {0} {1} {2}"
+ for r in query.execute(self.model):
+ yield msg.format(str(r['subject']),
+ str(r['predicate']),
+ str(r['object']))
+
+ def _validate_property_types(self):
+ """Find resources that don't have a type
+ """
+ property_template = """
+ prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+ prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+ select ?type
+ where {{
+ <{predicate}> a rdf:Property ;
+ {space} ?type .
+ }}"""
+
+ wrong_domain_type = "Domain of {0} {1} {2} not {3}"
+ wrong_range_type = "Range of {0} {1} {2} not {3}"
+
+ count = 0
+ schema = RDF.Node(RDF.Uri(SCHEMAS_URL))
+ for s, context in self.model.as_stream_context():
+ if context == schema:
+ continue
+ # check domain
+ query = RDF.SPARQLQuery(property_template.format(
+ predicate=s.predicate,
+ space='rdfs:domain'))
+ for r in query.execute(self.model):
+ if r['type'] == rdfsNS['Resource']:
+ continue
+ check = RDF.Statement(s.subject, rdfNS['type'], r['type'])
+ if not self.model.contains_statement(check):
+ yield wrong_domain_type.format(str(s.subject),
+ str(s.predicate),
+ str(s.object),
+ str(r['type']))
+ # check range
+ query = RDF.SPARQLQuery(property_template.format(
+ predicate=s.predicate,
+ space='rdfs:range'))
+ for r in query.execute(self.model):
+ if r['type'] == rdfsNS['Resource']:
+ continue
+ check = RDF.Statement(s.object, rdfNS['type'], r['type'])
+ if not self.model.contains_statement(check):
+ yield wrong_range_type.format(str(s.subject),
+ str(s.predicate),
+ str(s.object),
+ str(r['type']))
+
+ return
--- /dev/null
+"""Namespace definitions
+
+All in one place to make import rdfns.* work safely
+"""
+from RDF import NS
+
+# standard ontology namespaces
+rdfNS = NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
+rdfsNS = NS("http://www.w3.org/2000/01/rdf-schema#")
+owlNS = NS('http://www.w3.org/2002/07/owl#')
+dcNS = NS("http://purl.org/dc/elements/1.1/")
+xmlNS = NS('http://www.w3.org/XML/1998/namespace')
+xsdNS = NS("http://www.w3.org/2001/XMLSchema#")
+vsNS = NS('http://www.w3.org/2003/06/sw-vocab-status/ns#')
+wotNS = NS('http://xmlns.com/wot/0.1/')
+
+# internal ontologies
+submissionOntology = NS(
+ "http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#")
+dafTermOntology = NS("http://jumpgate.caltech.edu/wiki/UcscDaf#")
+libraryOntology = NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
+inventoryOntology = NS(
+ "http://jumpgate.caltech.edu/wiki/InventoryOntology#")
+submissionLog = NS("http://jumpgate.caltech.edu/wiki/SubmissionsLog/")
+geoSoftNS = NS('http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#')
--- /dev/null
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix dc: <http://purl.org/dc/elements/1.1/> .
+@prefix grddl: <http://www.w3.org/2003/g/data-view#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix vs: <http://www.w3.org/2003/06/sw-vocab-status/ns#> .
+@prefix foaf: <http://xmlns.com/foaf/0.1/> .
+@prefix wot: <http://xmlns.com/wot/0.1/> .
+
+# this is just a subset of dublin core
+<http://purl.org/dc/elements/1.1/>
+ dc:title "DCMI Metadata Terms" ;
+ rdfs:comment "Metadata terms maintained by the Dublin Core Metadata Initiative" ;
+ a owl:Ontology ;
+ rdfs:seeAlso <http://dublincore.org/documents/dcmi-terms/> .
+
+dc:title
+ a rdf:Property ;
+ rdfs:comment "A name given to the resource"@en ;
+ rdfs:range rdfs:Literal .
+
+dc:description
+ a rdf:Property ;
+ rdfs:label "Description"@en ;
+ rdfs:comment "An account of the resource"@en ;
+ rdfs:range rdfs:Literal .
--- /dev/null
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix dc: <http://purl.org/dc/elements/1.1/> .
+@prefix grddl: <http://www.w3.org/2003/g/data-view#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix vs: <http://www.w3.org/2003/06/sw-vocab-status/ns#> .
+@prefix foaf: <http://xmlns.com/foaf/0.1/> .
+@prefix wot: <http://xmlns.com/wot/0.1/> .
+
+
+<http://www.w3.org/2002/07/owl> a owl:Ontology ;
+ dc:title "The OWL 2 Schema vocabulary (OWL 2)" ;
+ rdfs:comment """
+ This ontology partially describes the built-in classes and
+ properties that together form the basis of the RDF/XML syntax of OWL 2.
+ The content of this ontology is based on Tables 6.1 and 6.2
+ in Section 6.4 of the OWL 2 RDF-Based Semantics specification,
+ available at http://www.w3.org/TR/owl2-rdf-based-semantics/.
+ Please note that those tables do not include the different annotations
+ (labels, comments and rdfs:isDefinedBy links) used in this file.
+ Also note that the descriptions provided in this ontology do not
+ provide a complete and correct formal description of either the syntax
+ or the semantics of the introduced terms (please see the OWL 2
+ recommendations for the complete and normative specifications).
+ Furthermore, the information provided by this ontology may be
+ misleading if not used with care. This ontology SHOULD NOT be imported
+ into OWL ontologies. Importing this file into an OWL 2 DL ontology
+ will cause it to become an OWL 2 Full ontology and may have other,
+ unexpected, consequences.
+ """ ;
+ rdfs:isDefinedBy
+ <http://www.w3.org/TR/owl2-mapping-to-rdf/>,
+ <http://www.w3.org/TR/owl2-rdf-based-semantics/>,
+ <http://www.w3.org/TR/owl2-syntax/> ;
+ rdfs:seeAlso <http://www.w3.org/TR/owl2-rdf-based-semantics/#table-axiomatic-classes>,
+ <http://www.w3.org/TR/owl2-rdf-based-semantics/#table-axiomatic-properties> ;
+ owl:imports <http://www.w3.org/2000/01/rdf-schema> ;
+ owl:versionIRI <http://www.w3.org/2002/07/owl> ;
+ owl:versionInfo "$Date: 2009/11/15 10:54:12 $" ;
+ # grddl:namespaceTransformation <http://dev.w3.org/cvsweb/2009/owl-grddl/owx2rdf.xsl>
+ .
+
+
+owl:AllDifferent a rdfs:Class ;
+ rdfs:label "AllDifferent" ;
+ rdfs:comment "The class of collections of pairwise different individuals." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf rdfs:Resource .
+
+owl:AllDisjointClasses a rdfs:Class ;
+ rdfs:label "AllDisjointClasses" ;
+ rdfs:comment "The class of collections of pairwise disjoint classes." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf rdfs:Resource .
+
+owl:AllDisjointProperties a rdfs:Class ;
+ rdfs:label "AllDisjointProperties" ;
+ rdfs:comment "The class of collections of pairwise disjoint properties." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf rdfs:Resource .
+
+owl:Annotation a rdfs:Class ;
+ rdfs:label "Annotation" ;
+ rdfs:comment "The class of annotated annotations for which the RDF serialization consists of an annotated subject, predicate and object." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf rdfs:Resource .
+
+owl:AnnotationProperty a rdfs:Class ;
+ rdfs:label "AnnotationProperty" ;
+ rdfs:comment "The class of annotation properties." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf rdf:Property .
+
+owl:AsymmetricProperty a rdfs:Class ;
+ rdfs:label "AsymmetricProperty" ;
+ rdfs:comment "The class of asymmetric properties." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf owl:ObjectProperty .
+
+owl:Axiom a rdfs:Class ;
+ rdfs:label "Axiom" ;
+ rdfs:comment "The class of annotated axioms for which the RDF serialization consists of an annotated subject, predicate and object." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf rdfs:Resource .
+
+owl:Class a rdfs:Class ;
+ rdfs:label "Class" ;
+ rdfs:comment "The class of OWL classes." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf rdfs:Class .
+
+owl:DataRange a rdfs:Class ;
+ rdfs:label "DataRange" ;
+ rdfs:comment "The class of OWL data ranges, which are special kinds of datatypes. Note: The use of the IRI owl:DataRange has been deprecated as of OWL 2. The IRI rdfs:Datatype SHOULD be used instead." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf rdfs:Datatype .
+
+owl:DatatypeProperty a rdfs:Class ;
+ rdfs:label "DatatypeProperty" ;
+ rdfs:comment "The class of data properties." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf rdf:Property .
+
+owl:DeprecatedClass a rdfs:Class ;
+ rdfs:label "DeprecatedClass" ;
+ rdfs:comment "The class of deprecated classes." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf rdfs:Class .
+
+owl:DeprecatedProperty a rdfs:Class ;
+ rdfs:label "DeprecatedProperty" ;
+ rdfs:comment "The class of deprecated properties." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf rdf:Property .
+
+owl:FunctionalProperty a rdfs:Class ;
+ rdfs:label "FunctionalProperty" ;
+ rdfs:comment "The class of functional properties." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf rdf:Property .
+
+owl:InverseFunctionalProperty a rdfs:Class ;
+ rdfs:label "InverseFunctionalProperty" ;
+ rdfs:comment "The class of inverse-functional properties." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf owl:ObjectProperty .
+
+owl:IrreflexiveProperty a rdfs:Class ;
+ rdfs:label "IrreflexiveProperty" ;
+ rdfs:comment "The class of irreflexive properties." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf owl:ObjectProperty .
+
+owl:NamedIndividual a rdfs:Class ;
+ rdfs:label "NamedIndividual" ;
+ rdfs:comment "The class of named individuals." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf owl:Thing .
+
+owl:NegativePropertyAssertion a rdfs:Class ;
+ rdfs:label "NegativePropertyAssertion" ;
+ rdfs:comment "The class of negative property assertions." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf rdfs:Resource .
+
+owl:Nothing a owl:Class ;
+ rdfs:label "Nothing" ;
+ rdfs:comment "This is the empty class." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf owl:Thing .
+
+owl:ObjectProperty a rdfs:Class ;
+ rdfs:label "ObjectProperty" ;
+ rdfs:comment "The class of object properties." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf rdf:Property .
+
+owl:Ontology a rdfs:Class ;
+ rdfs:label "Ontology" ;
+ rdfs:comment "The class of ontologies." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf rdfs:Resource .
+
+owl:OntologyProperty a rdfs:Class ;
+ rdfs:label "OntologyProperty" ;
+ rdfs:comment "The class of ontology properties." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf rdf:Property .
+
+owl:ReflexiveProperty a rdfs:Class ;
+ rdfs:label "ReflexiveProperty" ;
+ rdfs:comment "The class of reflexive properties." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf owl:ObjectProperty .
+
+owl:Restriction a rdfs:Class ;
+ rdfs:label "Restriction" ;
+ rdfs:comment "The class of property restrictions." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf owl:Class .
+
+owl:SymmetricProperty a rdfs:Class ;
+ rdfs:label "SymmetricProperty" ;
+ rdfs:comment "The class of symmetric properties." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf owl:ObjectProperty .
+
+owl:TransitiveProperty a rdfs:Class ;
+ rdfs:label "TransitiveProperty" ;
+ rdfs:comment "The class of transitive properties." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:subClassOf owl:ObjectProperty .
+
+owl:Thing a owl:Class , rdfs:Class ;
+ rdfs:label "Thing" ;
+ rdfs:comment "The class of OWL individuals." ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> .
+
+owl:allValuesFrom a rdf:Property ;
+ rdfs:label "allValuesFrom" ;
+ rdfs:comment "The property that determines the class that a universal property restriction refers to." ;
+ rdfs:domain owl:Restriction ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdfs:Class .
+
+owl:annotatedProperty a rdf:Property ;
+ rdfs:label "annotatedProperty" ;
+ rdfs:comment "The property that determines the predicate of an annotated axiom or annotated annotation." ;
+ rdfs:domain rdfs:Resource ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdfs:Resource .
+
+owl:annotatedSource a rdf:Property ;
+ rdfs:label "annotatedSource" ;
+ rdfs:comment "The property that determines the subject of an annotated axiom or annotated annotation." ;
+ rdfs:domain rdfs:Resource ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdfs:Resource .
+
+owl:annotatedTarget a rdf:Property ;
+ rdfs:label "annotatedTarget" ;
+ rdfs:comment "The property that determines the object of an annotated axiom or annotated annotation." ;
+ rdfs:domain rdfs:Resource ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdfs:Resource .
+
+owl:assertionProperty a rdf:Property ;
+ rdfs:label "assertionProperty" ;
+ rdfs:comment "The property that determines the predicate of a negative property assertion." ;
+ rdfs:domain owl:NegativePropertyAssertion ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdf:Property .
+
+owl:backwardCompatibleWith a owl:AnnotationProperty, owl:OntologyProperty ;
+ rdfs:label "backwardCompatibleWith" ;
+ rdfs:comment "The annotation property that indicates that a given ontology is backward compatible with another ontology." ;
+ rdfs:domain owl:Ontology ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range owl:Ontology .
+
+owl:bottomDataProperty a owl:DatatypeProperty ;
+ rdfs:label "bottomDataProperty" ;
+ rdfs:comment "The data property that does not relate any individual to any data value." ;
+ rdfs:domain owl:Thing ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdfs:Literal .
+
+owl:bottomObjectProperty a owl:ObjectProperty ;
+ rdfs:label "bottomObjectProperty" ;
+ rdfs:comment "The object property that does not relate any two individuals." ;
+ rdfs:domain owl:Thing ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range owl:Thing .
+
+owl:cardinality a rdf:Property ;
+ rdfs:label "cardinality" ;
+ rdfs:comment "The property that determines the cardinality of an exact cardinality restriction." ;
+ rdfs:domain owl:Restriction ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range xsd:nonNegativeInteger .
+
+owl:complementOf a rdf:Property ;
+ rdfs:label "complementOf" ;
+ rdfs:comment "The property that determines that a given class is the complement of another class." ;
+ rdfs:domain owl:Class ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range owl:Class .
+
+owl:datatypeComplementOf a rdf:Property ;
+ rdfs:label "datatypeComplementOf" ;
+ rdfs:comment "The property that determines that a given data range is the complement of another data range with respect to the data domain." ;
+ rdfs:domain rdfs:Datatype ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdfs:Datatype .
+
+owl:deprecated a owl:AnnotationProperty ;
+ rdfs:label "deprecated" ;
+ rdfs:comment "The annotation property that indicates that a given entity has been deprecated." ;
+ rdfs:domain rdfs:Resource ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdfs:Resource .
+
+owl:differentFrom a rdf:Property ;
+ rdfs:label "differentFrom" ;
+ rdfs:comment "The property that determines that two given individuals are different." ;
+ rdfs:domain owl:Thing ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range owl:Thing .
+
+owl:disjointUnionOf a rdf:Property ;
+ rdfs:label "disjointUnionOf" ;
+ rdfs:comment "The property that determines that a given class is equivalent to the disjoint union of a collection of other classes." ;
+ rdfs:domain owl:Class ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdf:List .
+
+owl:disjointWith a rdf:Property ;
+ rdfs:label "disjointWith" ;
+ rdfs:comment "The property that determines that two given classes are disjoint." ;
+ rdfs:domain owl:Class ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range owl:Class .
+
+owl:distinctMembers a rdf:Property ;
+ rdfs:label "distinctMembers" ;
+ rdfs:comment "The property that determines the collection of pairwise different individuals in a owl:AllDifferent axiom." ;
+ rdfs:domain owl:AllDifferent ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdf:List .
+
+owl:equivalentClass a rdf:Property ;
+ rdfs:label "equivalentClass" ;
+ rdfs:comment "The property that determines that two given classes are equivalent, and that is used to specify datatype definitions." ;
+ rdfs:domain rdfs:Class ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdfs:Class .
+
+owl:equivalentProperty a rdf:Property ;
+ rdfs:label "equivalentProperty" ;
+ rdfs:comment "The property that determines that two given properties are equivalent." ;
+ rdfs:domain rdf:Property ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdf:Property .
+
+owl:hasKey a rdf:Property ;
+ rdfs:label "hasKey" ;
+ rdfs:comment "The property that determines the collection of properties that jointly build a key." ;
+ rdfs:domain owl:Class ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdf:List .
+
+owl:hasSelf a rdf:Property ;
+ rdfs:label "hasSelf" ;
+ rdfs:comment "The property that determines the property that a self restriction refers to." ;
+ rdfs:domain owl:Restriction ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdfs:Resource .
+
+owl:hasValue a rdf:Property ;
+ rdfs:label "hasValue" ;
+ rdfs:comment "The property that determines the individual that a has-value restriction refers to." ;
+ rdfs:domain owl:Restriction ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdfs:Resource .
+
+owl:imports a owl:OntologyProperty ;
+ rdfs:label "imports" ;
+ rdfs:comment "The property that is used for importing other ontologies into a given ontology." ;
+ rdfs:domain owl:Ontology ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range owl:Ontology .
+
+owl:incompatibleWith a owl:AnnotationProperty, owl:OntologyProperty ;
+ rdfs:label "incompatibleWith" ;
+ rdfs:comment "The annotation property that indicates that a given ontology is incompatible with another ontology." ;
+ rdfs:domain owl:Ontology ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range owl:Ontology .
+
+owl:intersectionOf a rdf:Property ;
+ rdfs:label "intersectionOf" ;
+ rdfs:comment "The property that determines the collection of classes or data ranges that build an intersection." ;
+ rdfs:domain rdfs:Class ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdf:List .
+
+owl:inverseOf a rdf:Property ;
+ rdfs:label "inverseOf" ;
+ rdfs:comment "The property that determines that two given properties are inverse." ;
+ rdfs:domain owl:ObjectProperty ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range owl:ObjectProperty .
+
+owl:maxCardinality a rdf:Property ;
+ rdfs:label "maxCardinality" ;
+ rdfs:comment "The property that determines the cardinality of a maximum cardinality restriction." ;
+ rdfs:domain owl:Restriction ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range xsd:nonNegativeInteger .
+
+owl:maxQualifiedCardinality a rdf:Property ;
+ rdfs:label "maxQualifiedCardinality" ;
+ rdfs:comment "The property that determines the cardinality of a maximum qualified cardinality restriction." ;
+ rdfs:domain owl:Restriction ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range xsd:nonNegativeInteger .
+
+owl:members a rdf:Property ;
+ rdfs:label "members" ;
+ rdfs:comment "The property that determines the collection of members in either a owl:AllDifferent, owl:AllDisjointClasses or owl:AllDisjointProperties axiom." ;
+ rdfs:domain rdfs:Resource ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdf:List .
+
+owl:minCardinality a rdf:Property ;
+ rdfs:label "minCardinality" ;
+ rdfs:comment "The property that determines the cardinality of a minimum cardinality restriction." ;
+ rdfs:domain owl:Restriction ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range xsd:nonNegativeInteger .
+
+owl:minQualifiedCardinality a rdf:Property ;
+ rdfs:label "minQualifiedCardinality" ;
+ rdfs:comment "The property that determines the cardinality of a minimum qualified cardinality restriction." ;
+ rdfs:domain owl:Restriction ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range xsd:nonNegativeInteger .
+
+owl:onClass a rdf:Property ;
+ rdfs:label "onClass" ;
+ rdfs:comment "The property that determines the class that a qualified object cardinality restriction refers to." ;
+ rdfs:domain owl:Restriction ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range owl:Class .
+
+owl:onDataRange a rdf:Property ;
+ rdfs:label "onDataRange" ;
+ rdfs:comment "The property that determines the data range that a qualified data cardinality restriction refers to." ;
+ rdfs:domain owl:Restriction ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdfs:Datatype .
+
+owl:onDatatype a rdf:Property ;
+ rdfs:label "onDatatype" ;
+ rdfs:comment "The property that determines the datatype that a datatype restriction refers to." ;
+ rdfs:domain rdfs:Datatype ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdfs:Datatype .
+
+owl:oneOf a rdf:Property ;
+ rdfs:label "oneOf" ;
+ rdfs:comment "The property that determines the collection of individuals or data values that build an enumeration." ;
+ rdfs:domain rdfs:Class ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdf:List .
+
+owl:onProperties a rdf:Property ;
+ rdfs:label "onProperties" ;
+ rdfs:comment "The property that determines the n-tuple of properties that a property restriction on an n-ary data range refers to." ;
+ rdfs:domain owl:Restriction ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdf:List .
+
+owl:onProperty a rdf:Property ;
+ rdfs:label "onProperty" ;
+ rdfs:comment "The property that determines the property that a property restriction refers to." ;
+ rdfs:domain owl:Restriction ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdf:Property .
+
+owl:priorVersion a owl:AnnotationProperty, owl:OntologyProperty ;
+ rdfs:label "priorVersion" ;
+ rdfs:comment "The annotation property that indicates the predecessor ontology of a given ontology." ;
+ rdfs:domain owl:Ontology ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range owl:Ontology .
+
+owl:propertyChainAxiom a rdf:Property ;
+ rdfs:label "propertyChainAxiom" ;
+ rdfs:comment "The property that determines the n-tuple of properties that build a sub property chain of a given property." ;
+ rdfs:domain owl:ObjectProperty ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdf:List .
+
+owl:propertyDisjointWith a rdf:Property ;
+ rdfs:label "propertyDisjointWith" ;
+ rdfs:comment "The property that determines that two given properties are disjoint." ;
+ rdfs:domain rdf:Property ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdf:Property .
+
+owl:qualifiedCardinality a rdf:Property ;
+ rdfs:label "qualifiedCardinality" ;
+ rdfs:comment "The property that determines the cardinality of an exact qualified cardinality restriction." ;
+ rdfs:domain owl:Restriction ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range xsd:nonNegativeInteger .
+
+owl:sameAs a rdf:Property ;
+ rdfs:label "sameAs" ;
+ rdfs:comment "The property that determines that two given individuals are equal." ;
+ rdfs:domain owl:Thing ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range owl:Thing .
+
+owl:someValuesFrom a rdf:Property ;
+ rdfs:label "someValuesFrom" ;
+ rdfs:comment "The property that determines the class that an existential property restriction refers to." ;
+ rdfs:domain owl:Restriction ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdfs:Class .
+
+owl:sourceIndividual a rdf:Property ;
+ rdfs:label "sourceIndividual" ;
+ rdfs:comment "The property that determines the subject of a negative property assertion." ;
+ rdfs:domain owl:NegativePropertyAssertion ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range owl:Thing .
+
+owl:targetIndividual a rdf:Property ;
+ rdfs:label "targetIndividual" ;
+ rdfs:comment "The property that determines the object of a negative object property assertion." ;
+ rdfs:domain owl:NegativePropertyAssertion ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range owl:Thing .
+
+owl:targetValue a rdf:Property ;
+ rdfs:label "targetValue" ;
+ rdfs:comment "The property that determines the value of a negative data property assertion." ;
+ rdfs:domain owl:NegativePropertyAssertion ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdfs:Literal .
+
+owl:topDataProperty a owl:DatatypeProperty ;
+ rdfs:label "topDataProperty" ;
+ rdfs:comment "The data property that relates every individual to every data value." ;
+ rdfs:domain owl:Thing ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdfs:Literal .
+
+owl:topObjectProperty a owl:ObjectProperty ;
+ rdfs:label "topObjectProperty" ;
+ rdfs:comment "The object property that relates every two individuals." ;
+ rdfs:domain owl:Thing ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range owl:Thing .
+
+owl:unionOf a rdf:Property ;
+ rdfs:label "unionOf" ;
+ rdfs:comment "The property that determines the collection of classes or data ranges that build a union." ;
+ rdfs:domain rdfs:Class ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdf:List .
+
+owl:versionInfo a owl:AnnotationProperty ;
+ rdfs:label "versionInfo" ;
+ rdfs:comment "The annotation property that provides version information for an ontology or another OWL construct." ;
+ rdfs:domain rdfs:Resource ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdfs:Resource .
+
+owl:versionIRI a owl:OntologyProperty ;
+ rdfs:label "versionIRI" ;
+ rdfs:comment "The property that identifies the version IRI of an ontology." ;
+ rdfs:domain owl:Ontology ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range owl:Ontology .
+
+owl:withRestrictions a rdf:Property ;
+ rdfs:label "withRestrictions" ;
+ rdfs:comment "The property that determines the collection of facet-value pairs that define a datatype restriction." ;
+ rdfs:domain rdfs:Datatype ;
+ rdfs:isDefinedBy <http://www.w3.org/2002/07/owl#> ;
+ rdfs:range rdf:List .
--- /dev/null
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix dc: <http://purl.org/dc/elements/1.1/> .
+@prefix grddl: <http://www.w3.org/2003/g/data-view#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix vs: <http://www.w3.org/2003/06/sw-vocab-status/ns#> .
+@prefix foaf: <http://xmlns.com/foaf/0.1/> .
+@prefix wot: <http://xmlns.com/wot/0.1/> .
+
+<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+ dc:description "This is the RDF Schema for the RDF vocabulary defined in the RDF namespace."@en ;
+ dc:title "The RDF Vocabulary (RDF)"@en ;
+ a owl:Ontology ;
+ rdfs:seeAlso <http://www.w3.org/2000/01/rdf-schema-more> .
+
+rdf:Alt
+ a rdfs:Class ;
+ rdfs:comment "The class of containers of alternatives." ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "Alt" ;
+ rdfs:subClassOf rdfs:Container .
+
+rdf:Bag
+ a rdfs:Class ;
+ rdfs:comment "The class of unordered containers." ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "Bag" ;
+ rdfs:subClassOf rdfs:Container .
+
+rdf:List
+ a rdfs:Class ;
+ rdfs:comment "The class of RDF Lists." ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "List" ;
+ rdfs:subClassOf rdfs:Resource .
+
+rdf:PlainLiteral
+ a rdfs:Datatype ;
+ rdfs:comment "The class of plain (i.e. untyped) literal values." ;
+ rdfs:isDefinedBy <http://www.w3.org/TR/rdf-plain-literal/> ;
+ rdfs:label "PlainLiteral" ;
+ rdfs:subClassOf rdfs:Literal .
+
+rdf:Property
+ a rdfs:Class ;
+ rdfs:comment "The class of RDF properties." ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "Property" ;
+ rdfs:subClassOf rdfs:Resource .
+
+rdf:Seq
+ a rdfs:Class ;
+ rdfs:comment "The class of ordered containers." ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "Seq" ;
+ rdfs:subClassOf rdfs:Container .
+
+rdf:Statement
+ a rdfs:Class ;
+ rdfs:comment "The class of RDF statements." ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "Statement" ;
+ rdfs:subClassOf rdfs:Resource .
+
+rdf:XMLLiteral
+ a rdfs:Datatype ;
+ rdfs:comment "The class of XML literal values." ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "XMLLiteral" ;
+ rdfs:subClassOf rdfs:Literal .
+
+rdf:first
+ a rdf:Property ;
+ rdfs:comment "The first item in the subject RDF list." ;
+ rdfs:domain rdf:List ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "first" ;
+ rdfs:range rdfs:Resource .
+
+rdf:nil
+ a rdf:List ;
+ rdfs:comment "The empty list, with no items in it. If the rest of a list is nil then the list has no more items in it." ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "nil" .
+
+rdf:object
+ a rdf:Property ;
+ rdfs:comment "The object of the subject RDF statement." ;
+ rdfs:domain rdf:Statement ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "object" ;
+ rdfs:range rdfs:Resource .
+
+rdf:predicate
+ a rdf:Property ;
+ rdfs:comment "The predicate of the subject RDF statement." ;
+ rdfs:domain rdf:Statement ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "predicate" ;
+ rdfs:range rdfs:Resource .
+
+rdf:rest
+ a rdf:Property ;
+ rdfs:comment "The rest of the subject RDF list after the first item." ;
+ rdfs:domain rdf:List ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "rest" ;
+ rdfs:range rdf:List .
+
+rdf:subject
+ a rdf:Property ;
+ rdfs:comment "The subject of the subject RDF statement." ;
+ rdfs:domain rdf:Statement ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "subject" ;
+ rdfs:range rdfs:Resource .
+
+rdf:type
+ a rdf:Property ;
+ rdfs:comment "The subject is an instance of a class." ;
+ rdfs:domain rdfs:Resource ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "type" ;
+ rdfs:range rdfs:Class .
+
+rdf:value
+ a rdf:Property ;
+ rdfs:comment "Idiomatic property used for structured values." ;
+ rdfs:domain rdfs:Resource ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "value" ;
+ rdfs:range rdfs:Resource .
+
+<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+ dc:description "This is the RDF Schema for the RDF vocabulary defined in the RDF namespace."@en ;
+ dc:title "The RDF Vocabulary (RDF)"@en ;
+ a owl:Ontology ;
+ rdfs:seeAlso <http://www.w3.org/2000/01/rdf-schema-more> .
+
+rdf:Alt
+ a rdfs:Class ;
+ rdfs:comment "The class of containers of alternatives." ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "Alt" ;
+ rdfs:subClassOf rdfs:Container .
+
+rdf:Bag
+ a rdfs:Class ;
+ rdfs:comment "The class of unordered containers." ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "Bag" ;
+ rdfs:subClassOf rdfs:Container .
+
+rdf:List
+ a rdfs:Class ;
+ rdfs:comment "The class of RDF Lists." ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "List" ;
+ rdfs:subClassOf rdfs:Resource .
+
+rdf:PlainLiteral
+ a rdfs:Datatype ;
+ rdfs:comment "The class of plain (i.e. untyped) literal values." ;
+ rdfs:isDefinedBy <http://www.w3.org/TR/rdf-plain-literal/> ;
+ rdfs:label "PlainLiteral" ;
+ rdfs:subClassOf rdfs:Literal .
+
+rdf:Property
+ a rdfs:Class ;
+ rdfs:comment "The class of RDF properties." ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "Property" ;
+ rdfs:subClassOf rdfs:Resource .
+
+rdf:Seq
+ a rdfs:Class ;
+ rdfs:comment "The class of ordered containers." ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "Seq" ;
+ rdfs:subClassOf rdfs:Container .
+
+rdf:Statement
+ a rdfs:Class ;
+ rdfs:comment "The class of RDF statements." ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "Statement" ;
+ rdfs:subClassOf rdfs:Resource .
+
+rdf:XMLLiteral
+ a rdfs:Datatype ;
+ rdfs:comment "The class of XML literal values." ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "XMLLiteral" ;
+ rdfs:subClassOf rdfs:Literal .
+
+rdf:first
+ a rdf:Property ;
+ rdfs:comment "The first item in the subject RDF list." ;
+ rdfs:domain rdf:List ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "first" ;
+ rdfs:range rdfs:Resource .
+
+rdf:nil
+ a rdf:List ;
+ rdfs:comment "The empty list, with no items in it. If the rest of a list is nil then the list has no more items in it." ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "nil" .
+
+rdf:object
+ a rdf:Property ;
+ rdfs:comment "The object of the subject RDF statement." ;
+ rdfs:domain rdf:Statement ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "object" ;
+ rdfs:range rdfs:Resource .
+
+rdf:predicate
+ a rdf:Property ;
+ rdfs:comment "The predicate of the subject RDF statement." ;
+ rdfs:domain rdf:Statement ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "predicate" ;
+ rdfs:range rdfs:Resource .
+
+rdf:rest
+ a rdf:Property ;
+ rdfs:comment "The rest of the subject RDF list after the first item." ;
+ rdfs:domain rdf:List ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "rest" ;
+ rdfs:range rdf:List .
+
+rdf:subject
+ a rdf:Property ;
+ rdfs:comment "The subject of the subject RDF statement." ;
+ rdfs:domain rdf:Statement ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "subject" ;
+ rdfs:range rdfs:Resource .
+
+rdf:type
+ a rdf:Property ;
+ rdfs:comment "The subject is an instance of a class." ;
+ rdfs:domain rdfs:Resource ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "type" ;
+ rdfs:range rdfs:Class .
+
+rdf:value
+ a rdf:Property ;
+ rdfs:comment "Idiomatic property used for structured values." ;
+ rdfs:domain rdfs:Resource ;
+ rdfs:isDefinedBy <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ;
+ rdfs:label "value" ;
+ rdfs:range rdfs:Resource .
--- /dev/null
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix dc: <http://purl.org/dc/elements/1.1/> .
+@prefix grddl: <http://www.w3.org/2003/g/data-view#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix vs: <http://www.w3.org/2003/06/sw-vocab-status/ns#> .
+@prefix foaf: <http://xmlns.com/foaf/0.1/> .
+@prefix wot: <http://xmlns.com/wot/0.1/> .
+
+<http://www.w3.org/2000/01/rdf-schema#>
+ dc:title "The RDF Schema vocabulary (RDFS)" ;
+ a owl:Ontology ;
+ rdfs:seeAlso <http://www.w3.org/2000/01/rdf-schema-more> .
+
+rdfs:Class
+ a rdfs:Class ;
+ rdfs:comment "The class of classes." ;
+ rdfs:isDefinedBy <http://www.w3.org/2000/01/rdf-schema#> ;
+ rdfs:label "Class" ;
+ rdfs:subClassOf rdfs:Resource .
+
+rdfs:Container
+ a rdfs:Class ;
+ rdfs:comment "The class of RDF containers." ;
+ rdfs:isDefinedBy <http://www.w3.org/2000/01/rdf-schema#> ;
+ rdfs:label "Container" ;
+ rdfs:subClassOf rdfs:Resource .
+
+rdfs:ContainerMembershipProperty
+ a rdfs:Class ;
+ rdfs:comment """The class of container membership properties, rdf:_1, rdf:_2, ...,
+ all of which are sub-properties of 'member'.""" ;
+ rdfs:isDefinedBy <http://www.w3.org/2000/01/rdf-schema#> ;
+ rdfs:label "ContainerMembershipProperty" ;
+ rdfs:subClassOf rdf:Property .
+
+rdfs:Datatype
+ a rdfs:Class ;
+ rdfs:comment "The class of RDF datatypes." ;
+ rdfs:isDefinedBy <http://www.w3.org/2000/01/rdf-schema#> ;
+ rdfs:label "Datatype" ;
+ rdfs:subClassOf rdfs:Class .
+
+rdfs:Literal
+ a rdfs:Class ;
+ rdfs:comment "The class of literal values, eg. textual strings and integers." ;
+ rdfs:isDefinedBy <http://www.w3.org/2000/01/rdf-schema#> ;
+ rdfs:label "Literal" ;
+ rdfs:subClassOf rdfs:Resource .
+
+rdfs:Resource
+ a rdfs:Class ;
+ rdfs:comment "The class resource, everything." ;
+ rdfs:isDefinedBy <http://www.w3.org/2000/01/rdf-schema#> ;
+ rdfs:label "Resource" .
+
+rdfs:comment
+ a rdf:Property ;
+ rdfs:comment "A description of the subject resource." ;
+ rdfs:domain rdfs:Resource ;
+ rdfs:isDefinedBy <http://www.w3.org/2000/01/rdf-schema#> ;
+ rdfs:label "comment" ;
+ rdfs:range rdfs:Literal .
+
+rdfs:domain
+ a rdf:Property ;
+ rdfs:comment "A domain of the subject property." ;
+ rdfs:domain rdf:Property ;
+ rdfs:isDefinedBy <http://www.w3.org/2000/01/rdf-schema#> ;
+ rdfs:label "domain" ;
+ rdfs:range rdfs:Class .
+
+rdfs:isDefinedBy
+ a rdf:Property ;
+ rdfs:comment "The defininition of the subject resource." ;
+ rdfs:domain rdfs:Resource ;
+ rdfs:isDefinedBy <http://www.w3.org/2000/01/rdf-schema#> ;
+ rdfs:label "isDefinedBy" ;
+ rdfs:range rdfs:Resource ;
+ rdfs:subPropertyOf rdfs:seeAlso .
+
+rdfs:label
+ a rdf:Property ;
+ rdfs:comment "A human-readable name for the subject." ;
+ rdfs:domain rdfs:Resource ;
+ rdfs:isDefinedBy <http://www.w3.org/2000/01/rdf-schema#> ;
+ rdfs:label "label" ;
+ rdfs:range rdfs:Literal .
+
+rdfs:member
+ a rdf:Property ;
+ rdfs:comment "A member of the subject resource." ;
+ rdfs:domain rdfs:Resource ;
+ rdfs:isDefinedBy <http://www.w3.org/2000/01/rdf-schema#> ;
+ rdfs:label "member" ;
+ rdfs:range rdfs:Resource .
+
+rdfs:range
+ a rdf:Property ;
+ rdfs:comment "A range of the subject property." ;
+ rdfs:domain rdf:Property ;
+ rdfs:isDefinedBy <http://www.w3.org/2000/01/rdf-schema#> ;
+ rdfs:label "range" ;
+ rdfs:range rdfs:Class .
+
+rdfs:seeAlso
+ a rdf:Property ;
+ rdfs:comment "Further information about the subject resource." ;
+ rdfs:domain rdfs:Resource ;
+ rdfs:isDefinedBy <http://www.w3.org/2000/01/rdf-schema#> ;
+ rdfs:label "seeAlso" ;
+ rdfs:range rdfs:Resource .
+
+rdfs:subClassOf
+ a rdf:Property ;
+ rdfs:comment "The subject is a subclass of a class." ;
+ rdfs:domain rdfs:Class ;
+ rdfs:isDefinedBy <http://www.w3.org/2000/01/rdf-schema#> ;
+ rdfs:label "subClassOf" ;
+ rdfs:range rdfs:Class .
+
+rdfs:subPropertyOf
+ a rdf:Property ;
+ rdfs:comment "The subject is a subproperty of a property." ;
+ rdfs:domain rdf:Property ;
+ rdfs:isDefinedBy <http://www.w3.org/2000/01/rdf-schema#> ;
+ rdfs:label "subPropertyOf" ;
+ rdfs:range rdf:Property .
from datetime import datetime
from htsworkflow.util.rdfhelp import \
+ add_default_schemas, \
blankOrUri, \
+ dcNS, \
dump_model, \
fromTypedNode, \
get_model, \
guess_parser, \
guess_parser_by_extension, \
load_string_into_model, \
+ owlNS, \
+ rdfNS, \
rdfsNS, \
+ remove_schemas, \
toTypedNode, \
stripNamespace, \
simplify_uri, \
for contenttype, url, parser in DATA:
self.assertEqual(guess_parser(contenttype, url), parser)
+ class TestRDFSchemas(unittest.TestCase):
+ def test_rdf_schema(self):
+ """Does it basically work?
+ """
+ model = get_model()
+ self.assertEqual(model.size(), 0)
+ add_default_schemas(model)
+ self.assertGreater(model.size(), 0)
+ remove_schemas(model)
+ self.assertEqual(model.size(), 0)
+
+ def test_included_schemas(self):
+ model = get_model()
+ add_default_schemas(model)
+
+ # rdf test
+ s = RDF.Statement(rdfNS[''], dcNS['title'], None)
+ title = model.get_target(rdfNS[''], dcNS['title'])
+ self.assertTrue(title is not None)
+
+ s = RDF.Statement(rdfNS['Property'], rdfNS['type'], rdfsNS['Class'])
+ self.assertTrue(model.contains_statement(s))
+
+ # rdfs test
+ s = RDF.Statement(rdfsNS['Class'], rdfNS['type'], rdfsNS['Class'])
+ self.assertTrue(model.contains_statement(s))
+
+ s = RDF.Statement(owlNS['inverseOf'], rdfNS['type'],
+ rdfNS['Property'])
+ self.assertTrue(model.contains_statement(s))
+
+
def suite():
return unittest.makeSuite(TestRDFHelp, 'test')
except ImportError, e:
--- /dev/null
+import unittest
+
+import RDF
+
+from htsworkflow.util.rdfhelp import get_model, \
+ add_default_schemas, add_schema, load_string_into_model, dump_model
+from htsworkflow.util.rdfns import *
+from htsworkflow.util.rdfinfer import Infer
+
+foafNS = RDF.NS('http://xmlns.com/foaf/0.1/')
+
+MINI_FOAF_ONTOLOGY = """
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix foaf: <http://xmlns.com/foaf/0.1/> .
+
+
+foaf:Agent
+ a rdfs:Class, owl:Class ;
+ rdfs:comment "An agent (person, group, software or physical artifiact)."@en;
+ rdfs:label "Agent" .
+
+foaf:Person
+ a rdfs:Class, owl:Class, foaf:Agent ;
+ rdfs:label "Person" .
+
+foaf:age
+ a rdf:Property, owl:DatatypeProperty, owl:FunctionalProperty ;
+ rdfs:comment "The age in years of some agent." ;
+ rdfs:domain foaf:Agent ;
+ rdfs:label "age";
+ rdfs:range rdfs:Literal .
+
+foaf:familyName
+ a rdf:Property, owl:DatatypeProperty ;
+ rdfs:comment "Family name of some person." ;
+ rdfs:label "familyName" ;
+ rdfs:domain foaf:Person ;
+ rdfs:range rdfs:Literal .
+
+foaf:firstName
+ a rdf:Property, owl:DatatypeProperty ;
+ rdfs:comment "the first name of a person." ;
+ rdfs:domain foaf:Person ;
+ rdfs:label "firstname" ;
+ rdfs:range rdfs:Literal .
+
+foaf:Document
+ a rdfs:Class, owl:Class ;
+ rdfs:comment "A document." .
+
+foaf:Image
+ a rdfs:Class, owl:Class ;
+ rdfs:comment "An image." ;
+ rdfs:subClassOf foaf:Document .
+
+foaf:depicts
+ a rdf:Property, owl:ObjectProperty ;
+ rdfs:comment "A thing depicted in this representation." ;
+ rdfs:domain foaf:Image ;
+ rdfs:range owl:Thing ;
+ owl:inverseOf foaf:depiction .
+
+foaf:depiction
+ a rdf:Property, owl:ObjectProperty ;
+ rdfs:comment "Depiction of some thing." ;
+ rdfs:domain owl:Thing ;
+ rdfs:range foaf:Image ;
+ owl:inverseOf foaf:depicts .
+"""
+
+FOAF_DATA = """
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix foaf: <http://xmlns.com/foaf/0.1/> .
+
+_:me
+ foaf:firstName "Diane" ;
+ foaf:familyName "Trout" ;
+ a foaf:Person, owl:Thing ;
+ <http://example.org/other_literal> "value" ;
+ <http://example.org/other_resource> <http://example.org/resource> .
+
+<http://example.org/me.jpg>
+ a foaf:Image, owl:Thing ;
+ foaf:depicts _:me .
+"""
+
+class TestInfer(unittest.TestCase):
+ def setUp(self):
+ self.model = get_model()
+ add_default_schemas(self.model)
+ load_string_into_model(self.model, 'turtle', MINI_FOAF_ONTOLOGY)
+
+ def test_inverse_of(self):
+ fooNS = RDF.NS('http://example.org/')
+ load_string_into_model(self.model, 'turtle', FOAF_DATA)
+ inference = Infer(self.model)
+ depiction = RDF.Statement(None,
+ foafNS['depiction'],
+ fooNS['me.jpg'])
+ size = self.model.size()
+ found_statements = list(self.model.find_statements(depiction))
+ self.assertEqual(len(found_statements), 0)
+ inference._rule_inverse_of()
+ found_statements = list(self.model.find_statements(depiction))
+ self.assertEqual(len(found_statements), 1)
+
+ # we should've added one statement.
+ self.assertEqual(self.model.size(), size + 1)
+
+ size = self.model.size()
+ inference._rule_inverse_of()
+ # we should already have both versions in our model
+ self.assertEqual(self.model.size(), size)
+
+ def test_validate_types(self):
+ fooNS = RDF.NS('http://example.org/')
+ load_string_into_model(self.model, 'turtle', FOAF_DATA)
+ inference = Infer(self.model)
+
+ errors = list(inference._validate_types())
+ self.assertEqual(len(errors), 0)
+
+ s = RDF.Statement(fooNS['document'],
+ dcNS['title'],
+ RDF.Node("bleem"))
+ self.model.append(s)
+ errors = list(inference._validate_types())
+ self.assertEqual(len(errors), 1)
+
+ def test_validate_undefined_properties(self):
+ fooNS = RDF.NS('http://example.org/')
+ inference = Infer(self.model)
+
+ errors = list(inference._validate_undefined_properties())
+ self.assertEqual(len(errors), 0)
+
+ load_string_into_model(self.model, 'turtle', FOAF_DATA)
+
+ errors = list(inference._validate_undefined_properties())
+ self.assertEqual(len(errors), 2)
+
+
+ def test_validate_undefined_properties(self):
+ fooNS = RDF.NS('http://example.org/')
+ foafNS = RDF.NS('http://xmlns.com/foaf/0.1/')
+ load_string_into_model(self.model, 'turtle', FOAF_DATA)
+ inference = Infer(self.model)
+
+ errors = list(inference._validate_property_types())
+ self.assertEqual(len(errors), 0)
+
+ s = RDF.Statement(fooNS['me.jpg'],
+ foafNS['firstName'],
+ RDF.Node("name"))
+ self.model.append(s)
+ errors = list(inference._validate_property_types())
+ self.assertEqual(len(errors), 1)
+ self.assertTrue(errors[0].startswith('Domain of http://example.org'))
+ del self.model[s]
+
+ errors = list(inference._validate_property_types())
+ self.assertEqual(len(errors), 0)
+ s = RDF.Statement(fooNS['foo.txt'], rdfNS['type'], foafNS['Document'])
+ self.model.append(s)
+ s = RDF.Statement(fooNS['me.jpg'],
+ foafNS['depicts'],
+ foafNS['foo.txt'])
+ self.model.append(s)
+
+ errors = list(inference._validate_property_types())
+ self.assertEqual(len(errors), 1)
+ self.assertTrue(errors[0].startswith('Range of http://example.org'))
+ del self.model[s]
+
+def suite():
+ return unittest.makeSuite(TestInfer, 'test')
+
+if __name__ == "__main__":
+ unittest.main(defaultTest='suite')
-from setuptools import setup
+from setuptools import setup, find_packages
from version import get_git_version
setup(
description="Utilities to help manage high-through-put sequencing",
author="Diane Trout, Brandon King",
author_email="diane@caltech.edu",
- packages=["htsworkflow",
- "htsworkflow.automation",
- "htsworkflow.pipelines",
- "htsworkflow.util",
- # django site
- "htsworkflow.frontend",
- "htsworkflow.frontend.analysis",
- "htsworkflow.frontend.eland_config",
- "htsworkflow.frontend.experiments",
- "htsworkflow.frontend.inventory",
- "htsworkflow.frontend.reports",
- "htsworkflow.frontend.samples",
- ],
+ packages=find_packages(),
scripts=[
"scripts/htsw-copier",
"scripts/htsw-eland2bed",
"scripts/htsw-update-archive",
"scripts/htsw-validate",
],
+ package_data = {
+ '': ['*.turtle']
+ },
)
projects / htsworkflow.git / commitdiff