OWLPrime and Jena

Question

Hello,
System Specs:
Oracle 11g
Oracle Jena Adapter 2.0
Jena 2.5.6
I am trying to leverage the transitive, inverse, etc. properties of an ontology I downloaded. The ontology I am using references the Relationship Ontology (RO) from the OBO Foundry. The Relationship Ontology contains several transitive properties including the has_part property. I have a SPARQL query that I execute using Jena. My ontology contains some information in the form: A has_part B, A has_part C, B has_part D. Without creating any entailments, I was able to correctly query my ontology and get 2 results when I ran the query "SELECT * WHERE A has_part ?parts".
Now I want to take the next step and return the transitive cases where A has_part D (via the fact that B has_part D). To accomplish this, I loaded the "main ontology" along with the Relationship Ontology into an Oracle semantic model. Next, I ran the following through SQL*Plus to create the entailments: exec sem_apis.create_entailment(‘ontology_model_idx’,sem_models(‘ontology’), sem_rulebases(‘owlprime’));. The procedure ran fine without any errors. However, I still only get the same 2 results when I run "SELECT * WHERE A has_part ?parts". I am not returning the transitive cases. What else do I need to do? Do I need to add Pellet to my Jena code? If so, why? Aren't the inferences already in the Oracle table?
Thanks,
Chuck

Answer 1

Hi Alan,
I'm having a bit of trouble using my rule. First, I created my rule by executing the following commands from SQL*PLUS:
execute sem_apis.create_rulebase('user_rulebase');
INSERT INTO mdsys.semr_user_rulebase VALUES ('obo_has_part',
'(?whole <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?sub) (?sub <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Restriction>) (?sub <http://www.w3.org/2002/07/owl#onProperty> <http://www.obofoundry.org/ro/ro.owl#has_part>) (?sub <http://www.w3.org/2002/07/owl#someValuesFrom> ?part)', NULL, '(?whole <http://www.obofoundry.org/ro/ro.owl#has_part> ?part)', null);
Now I am trying to use the following code to execute my new rule along with the OWLPRIME rules from Java:
String[] rulelist = new String[2];
rulelist[0] = new String("OWLPRIME");
rulelist[1] = new String("USER_RULEBASE");
Attachment attachment = Attachment.createInstance(
Attachment.NO_ADDITIONAL_MODELS, rulelist,
InferenceMaintenanceMode.NO_UPDATE,
QueryOptions.DEFAULT);
graph.performInference();
graph.analyzeInferredGraph();
I am seeing the following output and errors:
INFO [main] (SimpleLog.java:49) - performInference: has valid entailment already
INFO [main] (SimpleLog.java:49) - Final clause = SELECT part$RDFVTYP, part$RDFLTYP, part$RDFLANG, part$RDFCLOB, decode(part$RDFVTYP, 'BLN', ('_:'||substr(part,instr(part,'m',4)+1)), part) part, whole$RDFVTYP, decode(whole$RDFVTYP, 'BLN', ('_:'||substr(whole,instr(whole,'m',4)+1)), whole) whole FROM table(sdo_rdf_match('(?whole <http://www.obofoundry.org/ro/ro.owl#has_part> ?part) ', sdo_rdf_models('NEURON_ONTOLOGY'), sdo_rdf_rulebases('OWLPRIME','USER_RULEBASE'), null, null, null))
Error: rethrew: java.sql.SQLException: ORA-20000: We do not have a rules index for this Model-Rulebase combination
ORA-06512: at "MDSYS.RDF_MATCH_IMPL_T", line 176
ORA-06512: at line 1
Do I need to run sem_apis.create_entailment?
Thanks,
Chuck