Examples with OWLDataProperty org.semanticweb.owlapi.model.OWLDataProperty used on opensource projects

Example 1 with OWLDataProperty

use of org.semanticweb.owlapi.model.OWLDataProperty in project goci by EBISPOT.

the class DefaultGWASOWLConverter method convertAssociation.

protected void convertAssociation(Association association, OWLOntology ontology, Set<String> issuedWarnings) {
    // get the trait association class
    OWLClass taClass = getDataFactory().getOWLClass(IRI.create(OntologyConstants.TRAIT_ASSOCIATION_CLASS_IRI));
    IRI taIndIRI = getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, association);
    // create a new trait association instance
    OWLNamedIndividual taIndiv = getDataFactory().getOWLNamedIndividual(taIndIRI);
    // assert class membership
    OWLClassAssertionAxiom classAssertion = getDataFactory().getOWLClassAssertionAxiom(taClass, taIndiv);
    getManager().addAxiom(ontology, classAssertion);
    // get datatype relations
    OWLDataProperty has_p_value = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_P_VALUE_PROPERTY_IRI));
    // get annotation relations
    OWLAnnotationProperty rdfsLabel = getDataFactory().getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
    //pvalue but says it was less then 10-6. So if we have no pvalue we just don't add it.
    if (association.getPvalueMantissa() != null && association.getPvalueExponent() != null) {
        double pval = association.getPvalueMantissa() * Math.pow(10, association.getPvalueExponent());
        OWLLiteral pValue = getDataFactory().getOWLLiteral(pval);
        //            OWLLiteral pValue = getDataFactory().getOWLLiteral(association.getPvalueMantissa()+"e"+association.getPvalueExponent());
        OWLDataPropertyAssertionAxiom p_value_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_p_value, taIndiv, pValue);
        AddAxiom add_p_value = new AddAxiom(ontology, p_value_relation);
        getManager().applyChange(add_p_value);
    }
    // get the snp instance for this association
    OWLNamedIndividual snpIndiv;
    String rsId = null;
    for (Locus locus : association.getLoci()) {
        for (RiskAllele riskAllele : locus.getStrongestRiskAlleles()) {
            SingleNucleotidePolymorphism snp = riskAllele.getSnp();
            rsId = snp.getRsId();
            snpIndiv = getDataFactory().getOWLNamedIndividual(getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, snp));
            if (snpIndiv == null) {
                String warning = "A new SNP with the given RSID only will be created";
                if (!issuedWarnings.contains(warning)) {
                    getLog().warn(warning);
                    issuedWarnings.add(warning);
                }
                snpIndiv = getDataFactory().getOWLNamedIndividual(getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, "SingleNucleotidePolymorphism", snp.getRsId(), true));
                // assert class membership
                OWLClass snpClass = getDataFactory().getOWLClass(IRI.create(OntologyConstants.SNP_CLASS_IRI));
                OWLClassAssertionAxiom snpClassAssertion = getDataFactory().getOWLClassAssertionAxiom(snpClass, snpIndiv);
                getManager().addAxiom(ontology, snpClassAssertion);
                // assert rsid relation
                OWLDataProperty has_snp_rsid = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_SNP_REFERENCE_ID_PROPERTY_IRI));
                OWLLiteral rsid = getDataFactory().getOWLLiteral(snp.getRsId());
                OWLDataPropertyAssertionAxiom rsid_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_snp_rsid, snpIndiv, rsid);
                AddAxiom add_rsid = new AddAxiom(ontology, rsid_relation);
                getManager().applyChange(add_rsid);
                // assert label
                OWLAnnotationAssertionAxiom snp_label_annotation = getDataFactory().getOWLAnnotationAssertionAxiom(rdfsLabel, snpIndiv.getIRI(), rsid);
                AddAxiom add_snp_label = new AddAxiom(ontology, snp_label_annotation);
                getManager().applyChange(add_snp_label);
            }
            // get object properties
            OWLObjectProperty has_subject = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.HAS_SUBJECT_IRI));
            OWLObjectProperty is_subject_of = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.IS_SUBJECT_OF_IRI));
            // assert relations
            OWLObjectPropertyAssertionAxiom has_subject_snp_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(has_subject, taIndiv, snpIndiv);
            AddAxiom add_has_subject_snp = new AddAxiom(ontology, has_subject_snp_relation);
            getManager().applyChange(add_has_subject_snp);
            OWLObjectPropertyAssertionAxiom is_subject_of_snp_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(is_subject_of, snpIndiv, taIndiv);
            AddAxiom add_is_subject_of_snp = new AddAxiom(ontology, is_subject_of_snp_relation);
            getManager().applyChange(add_is_subject_of_snp);
        }
        // get the EFO class for the trait
        for (EfoTrait efoTrait : association.getEfoTraits()) {
            OWLClass traitClass;
            traitClass = getDataFactory().getOWLClass(IRI.create(efoTrait.getUri()));
            if (traitClass == null) {
                String warning = "This trait will be mapped to Experimental Factor";
                if (!issuedWarnings.contains(warning)) {
                    getLog().warn(warning);
                    issuedWarnings.add(warning);
                }
                traitClass = getDataFactory().getOWLClass(IRI.create(OntologyConstants.EXPERIMENTAL_FACTOR_CLASS_IRI));
            }
            // create a new trait instance (puns the class)
            IRI traitIRI = traitClass.getIRI();
            OWLNamedIndividual traitIndiv = getDataFactory().getOWLNamedIndividual(traitIRI);
            if (ontology.containsIndividualInSignature(traitIRI)) {
                getLog().trace("Trait individual '" + traitIRI.toString() + "' (type: " + traitClass + ") already exists");
            } else {
                getLog().trace("Creating trait individual '" + traitIRI.toString() + "' (type: " + traitClass + ")");
            }
            // and also add the gwas label to the individual so we don't lose curated data
            OWLDataProperty has_gwas_trait_name = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_GWAS_TRAIT_NAME_PROPERTY_IRI));
            OWLLiteral gwasTrait = getDataFactory().getOWLLiteral(association.getStudy().getDiseaseTrait().getTrait());
            OWLDataPropertyAssertionAxiom gwas_trait_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_gwas_trait_name, taIndiv, gwasTrait);
            AddAxiom add_gwas_trait_name = new AddAxiom(ontology, gwas_trait_relation);
            getManager().applyChange(add_gwas_trait_name);
            // assert class membership
            OWLClassAssertionAxiom traitClassAssertion = getDataFactory().getOWLClassAssertionAxiom(traitClass, traitIndiv);
            getManager().addAxiom(ontology, traitClassAssertion);
            // get object properties
            OWLObjectProperty has_object = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.HAS_OBJECT_IRI));
            OWLObjectProperty is_object_of = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.IS_OBJECT_OF_IRI));
            // assert relations
            OWLObjectPropertyAssertionAxiom has_object_trait_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(has_object, taIndiv, traitIndiv);
            AddAxiom add_has_object_trait = new AddAxiom(ontology, has_object_trait_relation);
            getManager().applyChange(add_has_object_trait);
            OWLObjectPropertyAssertionAxiom is_object_of_trait_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(is_object_of, traitIndiv, taIndiv);
            AddAxiom add_is_object_of_trait = new AddAxiom(ontology, is_object_of_trait_relation);
            getManager().applyChange(add_is_object_of_trait);
        }
        // finally, assert label for this association
        OWLLiteral label = getDataFactory().getOWLLiteral("Association between " + rsId + " and " + association.getStudy().getDiseaseTrait().getTrait());
        OWLAnnotationAssertionAxiom label_annotation = getDataFactory().getOWLAnnotationAssertionAxiom(rdfsLabel, taIndiv.getIRI(), label);
        AddAxiom add_band_label = new AddAxiom(ontology, label_annotation);
        getManager().applyChange(add_band_label);
    }
}

Example 2 with OWLDataProperty

use of org.semanticweb.owlapi.model.OWLDataProperty in project goci by EBISPOT.

the class DefaultGWASOWLConverter method convertSNP.

protected void convertSNP(SingleNucleotidePolymorphism snp, OWLOntology ontology) {
    // get the snp class
    OWLClass snpClass = getDataFactory().getOWLClass(IRI.create(OntologyConstants.SNP_CLASS_IRI));
    // create a new snp instance
    OWLNamedIndividual snpIndiv = getDataFactory().getOWLNamedIndividual(getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, snp));
    // assert class membership
    OWLClassAssertionAxiom classAssertion = getDataFactory().getOWLClassAssertionAxiom(snpClass, snpIndiv);
    getManager().addAxiom(ontology, classAssertion);
    // add datatype properties...
    // get datatype relations
    OWLDataProperty has_snp_rsid = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_SNP_REFERENCE_ID_PROPERTY_IRI));
    OWLDataProperty has_bp_pos = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_BP_POSITION_PROPERTY_IRI));
    // get annotation relations
    OWLAnnotationProperty rdfsLabel = getDataFactory().getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
    // assert rsid relation
    OWLLiteral rsid = getDataFactory().getOWLLiteral(snp.getRsId());
    OWLDataPropertyAssertionAxiom rsid_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_snp_rsid, snpIndiv, rsid);
    AddAxiom add_rsid = new AddAxiom(ontology, rsid_relation);
    getManager().applyChange(add_rsid);
    // assert bp_pos relation
    if (snp.getLocations() != null) {
        for (Location snpLocation : snp.getLocations()) {
            if (snpLocation.getChromosomePosition() != null) {
                OWLLiteral bp_pos = //                            getDataFactory().getOWLLiteral(snpLocation.getChromosomePosition(), OWL2Datatype.XSD_INT);
                getDataFactory().getOWLLiteral(snpLocation.getChromosomePosition());
                OWLDataPropertyAssertionAxiom bp_pos_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_bp_pos, snpIndiv, bp_pos);
                AddAxiom add_bp_pos = new AddAxiom(ontology, bp_pos_relation);
                getManager().applyChange(add_bp_pos);
            }
        }
    } else {
        getLog().debug("No SNP location available for SNP " + rsid);
    }
    // assert label
    OWLAnnotationAssertionAxiom snp_label_annotation = getDataFactory().getOWLAnnotationAssertionAxiom(rdfsLabel, snpIndiv.getIRI(), rsid);
    AddAxiom add_snp_label = new AddAxiom(ontology, snp_label_annotation);
    getManager().applyChange(add_snp_label);
    // get the band class
    OWLClass bandClass = getDataFactory().getOWLClass(IRI.create(OntologyConstants.CYTOGENIC_REGION_CLASS_IRI));
    // get datatype relations
    OWLDataProperty has_name = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_NAME_PROPERTY_IRI));
    // get object relations
    OWLObjectProperty located_in = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.LOCATED_IN_PROPERTY_IRI));
    OWLObjectProperty location_of = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.LOCATION_OF_PROPERTY_IRI));
    // get datatype relations
    OWLDataProperty has_chr_name = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_NAME_PROPERTY_IRI));
    // get object properties
    OWLObjectProperty has_part = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.HAS_PART_PROPERTY_IRI));
    OWLObjectProperty part_of = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.PART_OF_PROPERTY_IRI));
    for (Location location : snp.getLocations()) {
        Region region = location.getRegion();
        if (region.getName() != null) {
            // create a new band individual
            OWLNamedIndividual bandIndiv = getDataFactory().getOWLNamedIndividual(getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, "CytogeneticRegion", region.getName()));
            // assert class membership
            OWLClassAssertionAxiom bandClassAssertion = getDataFactory().getOWLClassAssertionAxiom(bandClass, bandIndiv);
            getManager().addAxiom(ontology, bandClassAssertion);
            // assert name relation
            OWLLiteral name = getDataFactory().getOWLLiteral(region.getName());
            OWLDataPropertyAssertionAxiom name_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_name, bandIndiv, name);
            AddAxiom add_name = new AddAxiom(ontology, name_relation);
            getManager().applyChange(add_name);
            // assert label
            OWLAnnotationAssertionAxiom band_label_annotation = getDataFactory().getOWLAnnotationAssertionAxiom(rdfsLabel, bandIndiv.getIRI(), name);
            AddAxiom add_band_label = new AddAxiom(ontology, band_label_annotation);
            getManager().applyChange(add_band_label);
            // assert located_in relation
            OWLObjectPropertyAssertionAxiom located_in_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(located_in, snpIndiv, bandIndiv);
            AddAxiom add_located_in = new AddAxiom(ontology, located_in_relation);
            getManager().applyChange(add_located_in);
            // assert location_of relation
            OWLObjectPropertyAssertionAxiom location_of_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(location_of, bandIndiv, snpIndiv);
            AddAxiom add_location_of = new AddAxiom(ontology, location_of_relation);
            getManager().applyChange(add_location_of);
            // get the appropriate chromosome class given the chromosome name
            OWLClass chrClass = getDataFactory().getOWLClass(IRI.create(OntologyConstants.CHROMOSOME_CLASS_IRI));
            // create a new chromosome individual
            //If a snp has a chromosome name, create the chromosome individual if it doesn't have one (ex : the snp is
            // no mapped any more) then just don't create it.
            String chromName = location.getChromosomeName();
            if (chromName != null) {
                OWLNamedIndividual chrIndiv = getDataFactory().getOWLNamedIndividual(getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, "Chromosome", chromName));
                OWLClassAssertionAxiom chrClassAssertion = getDataFactory().getOWLClassAssertionAxiom(chrClass, chrIndiv);
                getManager().addAxiom(ontology, chrClassAssertion);
                // assert chr_name relation
                OWLLiteral chr_name = getDataFactory().getOWLLiteral(chromName);
                OWLDataPropertyAssertionAxiom chr_name_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_chr_name, chrIndiv, chr_name);
                AddAxiom add_chr_name = new AddAxiom(ontology, chr_name_relation);
                getManager().applyChange(add_chr_name);
                // assert label
                OWLLiteral chr_label = getDataFactory().getOWLLiteral("Chromosome " + chromName);
                OWLAnnotationAssertionAxiom chr_label_annotation = getDataFactory().getOWLAnnotationAssertionAxiom(rdfsLabel, chrIndiv.getIRI(), chr_label);
                AddAxiom add_chr_label = new AddAxiom(ontology, chr_label_annotation);
                getManager().applyChange(add_chr_label);
                // assert has_part relation
                OWLObjectPropertyAssertionAxiom has_part_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(has_part, chrIndiv, bandIndiv);
                AddAxiom add_has_part = new AddAxiom(ontology, has_part_relation);
                getManager().applyChange(add_has_part);
                // assert part_of relation
                OWLObjectPropertyAssertionAxiom part_of_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(part_of, bandIndiv, chrIndiv);
                AddAxiom add_part_of = new AddAxiom(ontology, part_of_relation);
                getManager().applyChange(add_part_of);
            }
        } else {
            getLog().trace("No known region for location on chromosomse " + location.getChromosomeName());
        }
    }
}

Example 3 with OWLDataProperty

use of org.semanticweb.owlapi.model.OWLDataProperty in project stanbol by apache.

the class TestUtils method checkProperties.

/**
	 * This is for monitoring hermit with datatype properties.
	 * 
	 * @param ont
	 */
public static void checkProperties(OWLOntology ont, Logger log) {
    // When throw inconsistent exception = false and ignoreUnsupportedDatatypes=true
    //- Datatypes which are not builtIn break the reasoner
    //- Looks like rdf:PlainLiteral is not supported by Hermit, even if it is marked as BuiltIn datatype by OWLApi
    // This incoherence generates an unexpected error!
    //
    Map<OWLDataProperty, Set<OWLDatatype>> properties = new HashMap<OWLDataProperty, Set<OWLDatatype>>();
    Set<OWLAxiom> remove = new HashSet<OWLAxiom>();
    for (OWLAxiom a : ont.getLogicalAxioms()) {
        if (a instanceof OWLDataPropertyAssertionAxiom) {
            OWLDataPropertyAssertionAxiom aa = (OWLDataPropertyAssertionAxiom) a;
            for (OWLDataProperty p : aa.getDataPropertiesInSignature()) {
                if (!properties.keySet().contains(p)) {
                    properties.put(p, new HashSet<OWLDatatype>());
                }
                for (OWLDatatype dt : aa.getDatatypesInSignature()) {
                    properties.get(p).add(dt);
                }
            }
        }
    }
    log.info("Data properties : ");
    for (Entry<OWLDataProperty, Set<OWLDatatype>> p : properties.entrySet()) {
        log.info(" - {} ", p.getKey());
        for (OWLDatatype d : p.getValue()) {
            log.info(" ---> {} [{}]", d, d.isBuiltIn());
        }
    }
    log.info("Data property axioms removed:");
    for (OWLAxiom d : remove) {
        log.info(" removed ---> {} ", d.getDataPropertiesInSignature());
    }
}

Example 4 with OWLDataProperty

use of org.semanticweb.owlapi.model.OWLDataProperty in project stanbol by apache.

the class RecipeListWriter method writeTo.

@Override
public void writeTo(RecipeList recipeList, Class<?> arg1, Type arg2, Annotation[] arg3, MediaType mediaType, MultivaluedMap<String, Object> arg5, OutputStream out) throws IOException, WebApplicationException {
    Logger log = LoggerFactory.getLogger(getClass());
    log.debug("Rendering the list of recipes.");
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    OWLDataFactory factory = OWLManager.getOWLDataFactory();
    OWLOntology ontology;
    try {
        ontology = manager.createOntology();
        String recipeClassURI = Symbols.Recipe.toString().replace("<", "").replace(">", "");
        IRI recipeClassIRI = IRI.create(recipeClassURI);
        OWLClass owlRecipeClass = factory.getOWLClass(recipeClassIRI);
        String descriptionURI = Symbols.description.toString().replace("<", "").replace(">", "");
        IRI descriptionIRI = IRI.create(descriptionURI);
        OWLDataProperty descriptionProperty = factory.getOWLDataProperty(descriptionIRI);
        if (recipeList != null) {
            log.info("Converting the recipe list to OWL.");
            for (Recipe recipe : recipeList) {
                String recipeURI = recipe.getRecipeID().toString().replace("<", "").replace(">", "");
                IRI recipeIRI = IRI.create(recipeURI);
                OWLIndividual recipeIndividual = factory.getOWLNamedIndividual(recipeIRI);
                OWLAxiom axiom = factory.getOWLClassAssertionAxiom(owlRecipeClass, recipeIndividual);
                manager.addAxiom(ontology, axiom);
                String description = recipe.getRecipeDescription();
                if (description != null) {
                    axiom = factory.getOWLDataPropertyAssertionAxiom(descriptionProperty, recipeIndividual, description);
                    manager.addAxiom(ontology, axiom);
                }
            }
        }
        if (mediaType.toString().equals(KRFormat.RDF_XML)) {
            try {
                manager.saveOntology(ontology, new RDFXMLOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.OWL_XML)) {
            try {
                manager.saveOntology(ontology, new OWLXMLOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.MANCHESTER_OWL)) {
            try {
                manager.saveOntology(ontology, new ManchesterOWLSyntaxOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.FUNCTIONAL_OWL)) {
            try {
                manager.saveOntology(ontology, new OWLFunctionalSyntaxOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.TURTLE)) {
            try {
                manager.saveOntology(ontology, new TurtleOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.RDF_JSON)) {
            Graph mGraph = OWLAPIToClerezzaConverter.owlOntologyToClerezzaGraph(ontology);
            RdfJsonSerializingProvider provider = new RdfJsonSerializingProvider();
            provider.serialize(out, mGraph, SupportedFormat.RDF_JSON);
        }
    } catch (OWLOntologyCreationException e1) {
        log.error("An error occurred.", e1);
    }
    out.flush();
}

Example 5 with OWLDataProperty

use of org.semanticweb.owlapi.model.OWLDataProperty in project stanbol by apache.

the class RecipeWriter method writeTo.

@Override
public void writeTo(Recipe recipe, Class<?> arg1, Type arg2, Annotation[] arg3, MediaType mediaType, MultivaluedMap<String, Object> arg5, OutputStream out) throws IOException, WebApplicationException {
    Logger log = LoggerFactory.getLogger(getClass());
    log.debug("Rendering the list of recipes.");
    if (mediaType.toString().equals(MediaType.TEXT_PLAIN)) {
        String recipeString = recipe.toString();
        out.write(recipeString.getBytes());
    } else if (mediaType.toString().equals(MediaType.TEXT_HTML)) {
        String recipeString = recipe.toString();
        out.write(recipeString.getBytes());
    } else {
        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
        OWLDataFactory factory = OWLManager.getOWLDataFactory();
        OWLOntology ontology;
        try {
            ontology = manager.createOntology();
            RuleList rules = recipe.getRuleList();
            IRI recipeID = recipe.getRecipeID();
            String recipeURI = recipeID.toString().replace("<", "").replace(">", "");
            org.semanticweb.owlapi.model.IRI recipeIRI = org.semanticweb.owlapi.model.IRI.create(recipeURI);
            OWLIndividual recipeIndividual = factory.getOWLNamedIndividual(recipeIRI);
            String descriptionURI = Symbols.description.toString().replace("<", "").replace(">", "");
            org.semanticweb.owlapi.model.IRI descriptionIRI = org.semanticweb.owlapi.model.IRI.create(descriptionURI);
            OWLDataProperty descriptionProperty = factory.getOWLDataProperty(descriptionIRI);
            OWLAxiom axiom;
            String recipeDescription = recipe.getRecipeDescription();
            if (recipeDescription != null) {
                axiom = factory.getOWLDataPropertyAssertionAxiom(descriptionProperty, recipeIndividual, recipeDescription);
                manager.addAxiom(ontology, axiom);
            }
            if (rules != null) {
                for (Rule rule : rules) {
                    IRI ruleID = rule.getRuleID();
                    String ruleName = rule.getRuleName();
                    String ruleDescription = rule.getDescription();
                    String ruleURI = ruleID.toString().replace("<", "").replace(">", "");
                    String ruleNameURI = Symbols.ruleName.toString().replace("<", "").replace(">", "");
                    String ruleBodyURI = Symbols.ruleBody.toString().replace("<", "").replace(">", "");
                    String ruleHeadURI = Symbols.ruleHead.toString().replace("<", "").replace(">", "");
                    String hasRuleURI = Symbols.hasRule.toString().replace("<", "").replace(">", "");
                    String ruleContent = rule.toString();
                    String[] ruleParts = ruleContent.split("\\->");
                    org.semanticweb.owlapi.model.IRI ruleIRI = org.semanticweb.owlapi.model.IRI.create(ruleURI);
                    org.semanticweb.owlapi.model.IRI ruleNameIRI = org.semanticweb.owlapi.model.IRI.create(ruleNameURI);
                    org.semanticweb.owlapi.model.IRI ruleBodyIRI = org.semanticweb.owlapi.model.IRI.create(ruleBodyURI);
                    org.semanticweb.owlapi.model.IRI ruleHeadIRI = org.semanticweb.owlapi.model.IRI.create(ruleHeadURI);
                    org.semanticweb.owlapi.model.IRI hasRuleIRI = org.semanticweb.owlapi.model.IRI.create(hasRuleURI);
                    OWLIndividual ruleIndividual = factory.getOWLNamedIndividual(ruleIRI);
                    OWLObjectProperty hasRule = factory.getOWLObjectProperty(hasRuleIRI);
                    OWLDataProperty nameProperty = factory.getOWLDataProperty(ruleNameIRI);
                    OWLDataProperty ruleBodyProperty = factory.getOWLDataProperty(ruleBodyIRI);
                    OWLDataProperty ruleHeadProperty = factory.getOWLDataProperty(ruleHeadIRI);
                    // add the name to the rule individual
                    axiom = factory.getOWLDataPropertyAssertionAxiom(nameProperty, ruleIndividual, ruleName);
                    manager.addAxiom(ontology, axiom);
                    // add the description to the rule individual
                    if (ruleDescription != null) {
                        axiom = factory.getOWLDataPropertyAssertionAxiom(descriptionProperty, ruleIndividual, ruleDescription);
                        manager.addAxiom(ontology, axiom);
                    }
                    // add the rule body to the rule individual
                    axiom = factory.getOWLDataPropertyAssertionAxiom(ruleBodyProperty, ruleIndividual, ruleParts[0]);
                    manager.addAxiom(ontology, axiom);
                    // add the rule head to the rule individual
                    axiom = factory.getOWLDataPropertyAssertionAxiom(ruleHeadProperty, ruleIndividual, ruleParts[1]);
                    manager.addAxiom(ontology, axiom);
                    // bind the rule to the recipe
                    axiom = factory.getOWLObjectPropertyAssertionAxiom(hasRule, recipeIndividual, ruleIndividual);
                    manager.addAxiom(ontology, axiom);
                }
            }
            if (mediaType.toString().equals(KRFormat.RDF_XML)) {
                try {
                    manager.saveOntology(ontology, new RDFXMLOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.OWL_XML)) {
                try {
                    manager.saveOntology(ontology, new OWLXMLOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.MANCHESTER_OWL)) {
                try {
                    manager.saveOntology(ontology, new ManchesterOWLSyntaxOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.FUNCTIONAL_OWL)) {
                try {
                    manager.saveOntology(ontology, new OWLFunctionalSyntaxOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.TURTLE)) {
                try {
                    manager.saveOntology(ontology, new TurtleOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.RDF_JSON)) {
                Graph mGraph = OWLAPIToClerezzaConverter.owlOntologyToClerezzaGraph(ontology);
                RdfJsonSerializingProvider provider = new RdfJsonSerializingProvider();
                provider.serialize(out, mGraph, SupportedFormat.RDF_JSON);
            }
        } catch (OWLOntologyCreationException e1) {
            log.error("An error occurred.", e1);
        }
    }
    out.flush();
}