jena_reasoner

Try to understand how ontology integration works in Apache Jena.

Two possibilities are investigated in this project:

via Apache Jena Fuseki, a SPARQL server
via Apache Jena API, a Java API

1. Data

Two samples with corresponding ontology data are tested:

	Sample data	Ontology
Pizza	`data/pizza.ttl`	`data/pizza_ontology.rdf`
Biology	`data/biology.ttl`	`data/biolink-model.owl.ttl`

1.1. Pizza

We focus on the inverse relationships defiend in OWL:

:isIngredientOf owl:inverseOf :hasIngredient .

i.e. the property isIngredientOf is the inverse of the property hasIngredient (see data/pizza_ontology.rdf).

Two pizza Margherita and Cheese Bacon: the relationship between a pizza and an ingredient is declared by the property either isIngredientOf or hasIngredient (see data/pizza.ttl). In summary:

Margherita contains tomato and basilic
Cheese Bacon contains cheese, bacon, and tomato

1.2. Biology

Biolink Model is a high level data model of biological entities and their associations in SWRL: a Semantic Web Rule Language Combining OWL and RuleML.

We focus on the inverse relationships:

biolink:catalyzes owl:inverseOf biolink:has_catalyst .

i.e. the property biolink:catalyzes is the inverse of the property biolink:has_catalyst (see data/biolink-model.owl.ttl).

Three biological reactions have corresponding catalysts (enzymes) and their relationships are declared by the property either biolink:catalyzes or biolink:has_catalyst (see data/biology.ttl). In summary:

ReactionA is catalyzed by EnzymeA1
ReactionB is catalyzed by EnzymeB1 and EnzymeB2
ReactionC is catalyzed by EnzymeC1 and EnzymeC2

2. Expected result

Initial missing information is complemented by ontology transitivity.

e.g. for Pizza, after a SPARQL query asking all triples ?pizza pizza:hasIngredient ?ingredient, initial missing information will be complemented because ex:tomato pizza:isIngredientOf ex:margherita is equivalent to ex:margherita pizza:hasIngredient ex:tomato.

3. Method

3.1. Fuseki

Each type of data (Pizza, Biology) is uploaded on TDB, a component of Jena for semantic data storage and query.
e.g. pizza_ontology.rdf is saved in /opt/tomcat/fuseki/base/databases/test_ontology_pizza.

Then a Fuseki's configuration is done according to Fuseki: Configuring Fuseki (section Inference) to integrate ontology. The configuration is the same as data/config.ttl.

All possible reasoners are tested:

Generic Rule Reasoner: http://jena.hpl.hp.com/2003/GenericRuleReasoner
Transitive Reasoner: http://jena.hpl.hp.com/2003/TransitiveReasoner
RDFS Rule Reasoner: http://jena.hpl.hp.com/2003/RDFSExptRuleReasoner
Full OWL Reasoner: http://jena.hpl.hp.com/2003/OWLFBRuleReasoner
Mini OWL Reasoner: http://jena.hpl.hp.com/2003/OWLMiniFBRuleReasoner
Micro OWL Reasoner: http://jena.hpl.hp.com/2003/OWLMicroFBRuleReasoner

Note: there is no reasoner for SWRL.

3.2. Jena API

Java codes are in src/Pizza.java and src/Biology.java.
For both case Jena used Full OWL Reasoner (OWLFBRuleReasoner).

4. Results

4.1. Fuseki

No ontology integration. Only raw information is retrieved:

# Pizza
[http://example.com/cheese_bacon, http://example.com/pizzas.owl#hasIngredient, http://example.com/tomato]
[http://example.com/cheese_bacon, http://example.com/pizzas.owl#hasIngredient, http://example.com/bacon]
[http://example.com/margherita, http://example.com/pizzas.owl#hasIngredient, http://example.com/basilic]

4.2. Jena API

The expected results are achieved.

--- In raw input pizza data ---
hasIngredient property
[http://example.com/cheese_bacon, http://example.com/pizzas.owl#hasIngredient, http://example.com/tomato]
[http://example.com/cheese_bacon, http://example.com/pizzas.owl#hasIngredient, http://example.com/bacon]
[http://example.com/margherita, http://example.com/pizzas.owl#hasIngredient, http://example.com/basilic]
isIngredientOf property
[http://example.com/cheese, http://example.com/pizzas.owl#isIngredientOf, http://example.com/cheese_bacon]
[http://example.com/tomato, http://example.com/pizzas.owl#isIngredientOf, http://example.com/margherita]

--- Results of SPARQL on raw model ---
( ?s = <http://example.com/cheese_bacon> ) ( ?o = <http://example.com/bacon> )
( ?s = <http://example.com/cheese_bacon> ) ( ?o = <http://example.com/tomato> )
( ?s = <http://example.com/margherita> ) ( ?o = <http://example.com/basilic> )

Binding ontology schema
    reasoner: org.apache.jena.reasoner.rulesys.OWLFBRuleReasoner@65004ff6
--- Results of SPARQL on inferred model ---
( ?s = <http://example.com/cheese_bacon> ) ( ?o = <http://example.com/bacon> )
( ?s = <http://example.com/cheese_bacon> ) ( ?o = <http://example.com/cheese> )
( ?s = <http://example.com/cheese_bacon> ) ( ?o = <http://example.com/tomato> )
( ?s = <http://example.com/margherita> ) ( ?o = <http://example.com/basilic> )
( ?s = <http://example.com/margherita> ) ( ?o = <http://example.com/tomato> )

--- In raw input biology data ---
has_catalyst property
[http://example.com/reactionB, https://w3id.org/biolink/vocab/has_catalyst, http://example.com/enzymeB1]
[http://example.com/reactionA, https://w3id.org/biolink/vocab/has_catalyst, http://example.com/enzymeA1]
catalyzes property
[http://example.com/enzymeC2, https://w3id.org/biolink/vocab/catalyzes, http://example.com/reactionC]
[http://example.com/enzymeC1, https://w3id.org/biolink/vocab/catalyzes, http://example.com/reactionC]
[http://example.com/enzymeB2, https://w3id.org/biolink/vocab/catalyzes, http://example.com/reactionB]

--- Results of SPARQL on raw model ---
( ?s = <http://example.com/reactionA> ) ( ?o = <http://example.com/enzymeA1> )
( ?s = <http://example.com/reactionB> ) ( ?o = <http://example.com/enzymeB1> )

Binding ontology schema
    reasoner: org.apache.jena.reasoner.rulesys.OWLFBRuleReasoner@1ddd3478
    duration: 00:00:59
Creating inference model
    duration: 00:00:00
--- Results of SPARQL on inferred model ---
( ?s = <http://example.com/reactionA> ) ( ?o = <http://example.com/enzymeA1> )
( ?s = <http://example.com/reactionB> ) ( ?o = <http://example.com/enzymeB1> )
( ?s = <http://example.com/reactionB> ) ( ?o = <http://example.com/enzymeB2> )
( ?s = <http://example.com/reactionC> ) ( ?o = <http://example.com/enzymeC1> )
( ?s = <http://example.com/reactionC> ) ( ?o = <http://example.com/enzymeC2> )
    duration: 00:00:00

5. Conclusion

The ontology inference was not successful on Fuseki server.
- The configuration file is not correctly applied.
- I need advice from the experts...!!!
Inference was successful via Jena API.
- For a big ontology data (Biolink Model), the step of bindSchema() is slow (around 1 minute)
- Full OWL Reasoner seems working on Biolink Model (SWRL format).

Future work

Merge/bind multiple ontology files to get a one ontology model
Save ontology model (then read it when needed)
Investigate whether Full OWL Reasoner reasoner application loses information of SWRL format

0m1n0/jena_reasoner