Configure Apache Jena RDF reasoner - sparql

I am trying to setup a reasoner for Apache Jena.
But I cannot get it working.
When I have a skos concept with skos:broader, I cannot query that concept by searching in the result by skos:narrower
Currently my config.ttl looks like see below.
Do I need to load the schema for skos in the configuration to make this work?
## Licensed under the terms of http://www.apache.org/licenses/LICENSE-2.0
#prefix : <#> .
#prefix fuseki: <http://jena.apache.org/fuseki#> .
#prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
#prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
#prefix tdb: <http://jena.hpl.hp.com/2008/tdb#> .
#prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .
## ---------------------------------------------------------------
## Service with only SPARQL query on an inference model.
## Inference model base data is in TDB.
<#service2> rdf:type fuseki:Service ;
rdfs:label "skos" ;
fuseki:name "skos" ;
fuseki:serviceQuery "sparql" ; # SPARQL query service
fuseki:serviceUpdate "update" ;
fuseki:dataset <#dataset> ;
.
<#dataset> rdf:type ja:RDFDataset ;
ja:defaultGraph <#model_inf> ;
.
<#model_inf> a ja:InfModel ;
ja:baseModel <#tdbGraph> ;
ja:reasoner [
ja:reasonerURL <http://jena.hpl.hp.com/2003/RDFSExptRuleReasoner>
] .
## Base data in TDB.
<#tdbDataset> rdf:type tdb:DatasetTDB ;
tdb:location "run/databases/skos" ;
# If the unionDefaultGraph is used, then the "update" service should be removed.
# tdb:unionDefaultGraph true ;
.
<#tdbGraph> rdf:type tdb:GraphTDB ;
tdb:dataset <#tdbDataset> .
My data would look something like this.
I would expect the example.com/1 to have example.com/2 as narrower as it is the inverse of broader.
<http://example.com/2>
a skos:Concept ;
skos:broader <http://example.com/1> ;
skos:prefLabel "schaapskooi"#nl .
<http://example.com/1>
a skos:Concept ;
skos:prefLabel "restant landschapstermen"#nl ;

Related

Fuseki Named Graph persistence with inference

I am trying to persist multiple named graphs with inference in Fuseki.
I am referring to this excellent article, but facing some issues in Scenario 2: named graphs and no online updates.
My assembler configuration looks like this:
#prefix : <#> .
#prefix fuseki: <http://jena.apache.org/fuseki#> .
#prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
#prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
#prefix tdb: <http://jena.hpl.hp.com/2008/tdb#> .
#prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .
## ---------------------------------------------------------------
## Updatable TDB dataset with all services enabled.
:service_tdb_all rdf:type fuseki:Service ;
rdfs:label "TDB onekg-metadata-dev" ;
fuseki:name "onekg-metadata-dev" ;
fuseki:serviceQuery "" ;
fuseki:serviceQuery "sparql" ;
fuseki:serviceQuery "query" ;
fuseki:serviceUpdate "" ;
fuseki:serviceUpdate "update" ;
fuseki:serviceUpload "upload" ;
fuseki:serviceReadWriteGraphStore "data" ;
fuseki:serviceReadGraphStore "get" ;
fuseki:dataset :dataset ;
.
# Location of the TDB dataset
:tdb_dataset_readwrite
a tdb:DatasetTDB ;
tdb:location "reasoning-dir" ;
.
# Inference dataset
:dataset a ja:RDFDataset ;
ja:defaultGraph :model_inf .
# Inference Model
:model_inf a ja:InfModel ;
ja:baseModel :graph ;
ja:reasoner [
ja:reasonerURL
<http://jena.hpl.hp.com/2003/OWLFBRuleReasoner>
] .
# Intermediate graph referencing to the union graph
:graph rdf:type tdb:GraphTDB ;
tdb:dataset :tdb_dataset_readwrite ;
.
I am uploading some triples in a named graph and can query the triples(without inference) as is expected.
However, if I try to restart and try to query again, the named graph is missing and I can not query anything from there.
I would like to get some help here. Thank you in advance.

SPARQL Inference with SKOS

We are trying to showcase inference with linked-data.
The simple graph looks like the following in turtle-format:
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ex: <http://schema.example.com/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
ex:Places rdf:type skos:ConceptScheme .
ex:Localities rdf:type skos:Concept .
ex:Localities skos:prefLabel "Localities" .
ex:Localities skos:inScheme ex:Places.
ex:Countries rdf:type skos:Concept .
ex:Countries skos:prefLabel "Countries" .
ex:Countries skos:inScheme ex:Places.
ex:Continents rdf:type skos:Concept .
ex:Continents skos:prefLabel "Continents" .
ex:Continents skos:inScheme ex:Places.
ex:Persons rdf:type skos:Concept .
ex:Persons skos:prefLabel "Persons" .
ex:livesIn a rdf:Property .
ex:isPartOf a rdf:Property .
ex:Localities skos:broader ex:Countries .
ex:Countries skos:broader ex:Continents .
ex:Europe a ex:Continents .
ex:Switzerland a ex:Countries .
ex:Switzerland ex:isPartOf ex:Europe.
ex:France a ex:Countries .
ex:France ex:isPartOf ex:Europe.
ex:Bern a ex:Localities .
ex:Bern skos:prefLabel "Bern".
ex:Bern ex:isPartOf ex:Switzerland.
ex:Thun a ex:Localities .
ex:Thun skos:prefLabel "Thun".
ex:Thun ex:isPartOf ex:Switzerland.
ex:Paris a ex:Localities .
ex:Paris skos:prefLabel "Paris".
ex:Paris ex:isPartOf ex:France.
ex:Hans a ex:Persons.
ex:Hans skos:prefLabel "Hans".
ex:Hans ex:livesIn ex:Bern.
ex:Fritz a ex:Persons.
ex:Frits skos:prefLabel "Fritz".
ex:Fritz ex:livesIn ex:Thun.
ex:Jaques a ex:Persons.
ex:Jaques skos:prefLabel "Jaques".
ex:Jaques ex:livesIn ex:Paris.
The Idea would be to do the following query in SPARQL:
PREFIX ex: <http://schema.example.com/>
ASK where { ex:Hans ex:livesIn ex:Switzerland }
It should return YES, but it returns NO.
Is there a possibility to model the data, that this ASK-Statement can get answered with YES?
In terms of inference it should be True, since ex:Bern is a ex:Localities and this is a skos:broader of ex:Countries, which is ex:Switzerland.
I haven't found any good examples for skos-Modelling and Inference yet.
We would like to work with skos:concepts and rather not with rdfs-subclassing.
Because it should showcase the inference over concepts in situations, where you are not able to subclass everything.
I am using:
GraphDB 9.5.0 EE
OWL2-RL - Ruleset
To complete the question, I'm posting my comment above as an answer...
To make it work, You need to define some meaning to your properties ex:isPartOf and ex:livesIn.
Suggest to make ex:isPartOf transitive and then to define ex:livesIn as a property chain over ex:isPartOf, e.g.:
ex:isPartOf a owl:TransitiveProperty .
ex:livesIn rdf:type owl:ObjectProperty;
owl:propertyChainAxiom( ex:livesIn ex:isPartOf) .

OWL/owlapi: Get Individuals with "unsatisfied" Object Properties

I'm working with an OWL Ontology in Protégé 5.1.0 (plus HermiT 1.3.8.413 Reasoner) that I later want to use with OWLAPI 4.1.0 and maybe DL-Query or SPARQL. My task at hand is to get all Individuals of a class that have a certain Object Property unfulfilled. Because of the open-world assumption, an unfulfilled Object Property doesn't usually show up as a problem, but I need the information and would like to avoid writing my own code to check the whole ontology.
I prepared I small example, as readable text and Turtle-code:
Classes: Pizza, Topping
Object Property: has
Assertion: Pizza has some Topping
Individuals: Pizza1, Pizza2, Topping1, Topping2 (of respective Classes)
Assertion: Pizza1 has Topping1
Code:
#prefix : <http://www.semanticweb.org/user/ontologies/2017/0/untitled-ontology-23#> .
#prefix owl: <http://www.w3.org/2002/07/owl#> .
#prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
#prefix xml: <http://www.w3.org/XML/1998/namespace> .
#prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
#prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
#base <http://www.semanticweb.org/user/ontologies/2017/0/untitled-ontology-23> .
<http://www.semanticweb.org/user/ontologies/2017/0/untitled-ontology-23> rdf:type owl:Ontology .
#################################################################
# Object Properties
#################################################################
### http://www.semanticweb.org/user/ontologies/2017/0/untitled-ontology-23#has
:has rdf:type owl:ObjectProperty ;
owl:inverseOf :isOn .
### http://www.semanticweb.org/user/ontologies/2017/0/untitled-ontology-23#isOn
:isOn rdf:type owl:ObjectProperty ,
owl:FunctionalProperty .
#################################################################
# Classes
#################################################################
### http://www.semanticweb.org/user/ontologies/2017/0/untitled-ontology-23#Pizza
:Pizza rdf:type owl:Class ;
rdfs:subClassOf [ rdf:type owl:Restriction ;
owl:onProperty :has ;
owl:someValuesFrom :Topping
] .
### http://www.semanticweb.org/user/ontologies/2017/0/untitled-ontology-23#Topping
:Topping rdf:type owl:Class .
#################################################################
# Individuals
#################################################################
### http://www.semanticweb.org/user/ontologies/2017/0/untitled-ontology-23#Pizza1
:Pizza1 rdf:type owl:NamedIndividual ,
:Pizza ;
:has :Topping1 .
### http://www.semanticweb.org/user/ontologies/2017/0/untitled-ontology-23#Pizza2
:Pizza2 rdf:type owl:NamedIndividual ,
:Pizza .
### http://www.semanticweb.org/user/ontologies/2017/0/untitled-ontology-23#Topping1
:Topping1 rdf:type owl:NamedIndividual ,
:Topping ;
:isOn :Pizza1 .
### http://www.semanticweb.org/user/ontologies/2017/0/untitled-ontology-23#Topping2
:Topping2 rdf:type owl:NamedIndividual ,
:Topping .
#################################################################
# General axioms
#################################################################
[ rdf:type owl:AllDifferent ;
owl:distinctMembers ( :Pizza1
:Pizza2
)
] .
[ rdf:type owl:AllDifferent ;
owl:distinctMembers ( :Topping1
:Topping2
)
] .
### Generated by the OWL API (version 4.2.6.20160910-2108) https://github.com/owlcs/owlapi
In this case, I would like to query the ontology and get the information that Pizza2 currently doesn't have any Topping, i.e. its Object Property is not asserted or inferred. Also, if Topping1 is changed to be of a different class, I now want to see Pizza1 show up in the query as well because "Pizza has some Topping" is unsatisfied.
Is there an elegant way to do this either directly in OWLAPI or using DL-Query/SPARQL?

Currently in a locked region: Fuseki + full text search + inference

I've recently started playing with the full text search in the Fuseki 0.2.8 snapshot.
I have an InfModel backed by a TDB dataset, which I've added a Lucene text index to. I have tested it out with some search queries like this:
prefix text: <http://jena.apache.org/text#>
select distinct ?s where { ?s text:query ('stu' 16) }
This works great, until I have two or more simultaneous queries to Fuseki, then occasionally I get:
Error 500: Currently in a locked region Fuseki - version 0.2.8-SNAPSHOT (Build date: 20130820-0755).
I've tried testing out the endpoint with 10 concurrent users sending queries at random intervals, over a two minute period around 30% of the queries return the 500 error above.
I have also tried disabling inference by replacing this section (full assembler file below):
<#dataset_fulltext> rdf:type text:TextDataset ;
text:dataset <#dataset_inf> ;
##text:dataset <#tdbDataset> ;
text:index <#indexLucene> .
with this:
<#dataset_fulltext> rdf:type text:TextDataset ;
##text:dataset <#dataset_inf> ;
text:dataset <#tdbDataset> ;
text:index <#indexLucene> .
and there are no exceptions generated when the TextDataset is using #tdbDataset rather than #dataset_inf.
Are there any problems with my set up, or is this a bug in Fuseki?
Here is my current assembler file:
#prefix : <#> .
#prefix fuseki: <http://jena.apache.org/fuseki#> .
#prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
#prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
#prefix tdb: <http://jena.hpl.hp.com/2008/tdb#> .
#prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .
#prefix text: <http://jena.apache.org/text#> .
#prefix dc: <http://purl.org/dc/terms/> .
[] rdf:type fuseki:Server ;
# Timeout - server-wide default: milliseconds.
# Format 1: "1000" -- 1 second timeout
# Format 2: "10000,60000" -- 10s timeout to first result, then 60s timeout to for rest of query.
# See java doc for ARQ.queryTimeout
ja:context [ ja:cxtName "arq:queryTimeout" ; ja:cxtValue "12000,50000" ] ;
fuseki:services (
<#service1>
) .
# Custom code.
[] ja:loadClass "com.hp.hpl.jena.tdb.TDB" .
# TDB
tdb:DatasetTDB rdfs:subClassOf ja:RDFDataset .
tdb:GraphTDB rdfs:subClassOf ja:Model .
## Initialize text query
[] ja:loadClass "org.apache.jena.query.text.TextQuery" .
# A TextDataset is a regular dataset with a text index.
text:TextDataset rdfs:subClassOf ja:RDFDataset .
# Lucene index
text:TextIndexLucene rdfs:subClassOf text:TextIndex .
## ---------------------------------------------------------------
## Service with only SPARQL query on an inference model.
## Inference model bbase data in TDB.
<#service1> rdf:type fuseki:Service ;
rdfs:label "TDB/text service" ;
fuseki:name "dataset" ; # http://host/dataset
fuseki:serviceQuery "query" ;
fuseki:serviceUpdate "update" ;
fuseki:serviceUpload "upload" ;
fuseki:serviceReadWriteGraphStore "data" ;
fuseki:serviceReadGraphStore "get" ;
fuseki:dataset <#dataset_fulltext> ;
.
<#dataset_inf> rdf:type ja:RDFDataset ;
ja:defaultGraph <#model_inf> .
<#model_inf> rdf:type ja:Model ;
ja:baseModel <#tdbGraph> ;
ja:reasoner [ ja:reasonerURL <http://jena.hpl.hp.com/2003/OWLMicroFBRuleReasoner> ] .
<#tdbDataset> rdf:type tdb:DatasetTDB ;
tdb:location "Data" .
<#tdbGraph> rdf:type tdb:GraphTDB ;
tdb:dataset <#tdbDataset> .
# Dataset with full text index.
<#dataset_fulltext> rdf:type text:TextDataset ;
text:dataset <#dataset_inf> ;
##text:dataset <#tdbDataset> ;
text:index <#indexLucene> .
# Text index description
<#indexLucene> a text:TextIndexLucene ;
text:directory <file:Lucene> ;
##text:directory "mem" ;
text:entityMap <#entMap> ;
.
# Mapping in the index
# URI stored in field "uri"
# rdfs:label is mapped to field "text"
<#entMap> a text:EntityMap ;
text:entityField "uri" ;
text:defaultField "text" ;
text:map (
[ text:field "text" ; text:predicate dc:title ]
[ text:field "text" ; text:predicate dc:description ]
) .
And here is the full stack trace for one of the exceptions in Fuseki's log:
16:27:01 WARN Fuseki :: [2484] RC = 500 : Currently in a locked region
com.hp.hpl.jena.sparql.core.DatasetGraphWithLock$JenaLockException: Currently in a locked region
at com.hp.hpl.jena.sparql.core.DatasetGraphWithLock.checkNotActive(DatasetGraphWithLock.java:72)
at com.hp.hpl.jena.sparql.core.DatasetGraphTrackActive.begin(DatasetGraphTrackActive.java:44)
at org.apache.jena.query.text.DatasetGraphText.begin(DatasetGraphText.java:102)
at org.apache.jena.fuseki.servlets.HttpAction.beginRead(HttpAction.java:117)
at org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:236)
at org.apache.jena.fuseki.servlets.SPARQL_Query.executeWithParameter(SPARQL_Query.java:195)
at org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:80)
at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeLifecycle(SPARQL_ServletBase.java:185)
at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeAction(SPARQL_ServletBase.java:166)
at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.execCommonWorker(SPARQL_ServletBase.java:154)
at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.doCommon(SPARQL_ServletBase.java:73)
at org.apache.jena.fuseki.servlets.SPARQL_Query.doGet(SPARQL_Query.java:61)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:735)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1448)
at org.eclipse.jetty.servlets.UserAgentFilter.doFilter(UserAgentFilter.java:82)
at org.eclipse.jetty.servlets.GzipFilter.doFilter(GzipFilter.java:294)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1419)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:455)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:229)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1075)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:384)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1009)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
at org.eclipse.jetty.server.Server.handle(Server.java:370)
at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:489)
at org.eclipse.jetty.server.BlockingHttpConnection.handleRequest(BlockingHttpConnection.java:53)
at org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:949)
at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:1011)
at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:644)
at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
at org.eclipse.jetty.server.BlockingHttpConnection.handle(BlockingHttpConnection.java:72)
at org.eclipse.jetty.server.nio.BlockingChannelConnector$BlockingChannelEndPoint.run(BlockingChannelConnector.java:298)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
at java.lang.Thread.run(Thread.java:722)
Any advice appreciated.
Thanks,
Stuart.
This looks like it is probably a bug which I have filed as JENA-522, if you have further details on the bug to add please add a comment there.
The issue is that the dataset with inference implicitly uses ARQ's standard in-memory Dataset implementation and this does not support transactions.
However text datasets which correspond to DatasetGraphText internally (and in your stack trace) requires the wrapped dataset to support transactions and where they do not wraps them with DatasetGraphWithLock. It is this that appears to be encountering the problem with the lock, the documentation states that this should support multiple readers but having followed the logic of the code I'm not sure that it actually allows this.

Can I configure Jena Fuseki with inference and TDB?

I want to configure Fuseki with an inference model supported by TDB.
I have been able to configure it with a Memory Model, but not with a TDB Model where I could update triples.
I am using the following assembler description:
#prefix tdb: <http://jena.hpl.hp.com/2008/tdb#> .
#prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
#prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
#prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .
#prefix tdb: <http://jena.hpl.hp.com/2008/tdb#> .
[] ja:loadClass "com.hp.hpl.jena.tdb.TDB" .
tdb:DatasetTDB rdfs:subClassOf ja:RDFDataset .
tdb:GraphTDB rdfs:subClassOf ja:Model .
<#dataset> rdf:type ja:RDFDataset ;
ja:defaultGraph <#infModel> .
<#infModel> a ja:InfModel ;
ja:baseModel <#tdbGraph>;
ja:reasoner
[ja:reasonerURL <http://jena.hpl.hp.com/2003/RDFSExptRuleReasoner>].
<#tdbGraph> rdf:type tdb:GraphTDB ;
tdb:location "DB" ;
.
It works fine and it is able to do RDFS inference and even to insert new triples.
However, once I stop and restart the server, it raises the following exception:
Error 500: Invalid id node for subject (null node): ([000000000000001D], [00000000000000AF], [000000000000003D])
<#tdbGraph> rdf:type tdb:GraphTDB ;
tdb:location "DB" ;
.
Get rid of the semi colon after the second statement and terminate with the full stop ie:
<#tdbGraph> rdf:type tdb:GraphTDB ;
tdb:location "DB".