SPARQL ftw!

construct

PREFIX belv: <http://www.openbel.org/vocabulary/>
PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>

CONSTRUCT {
    ?s        rdf:type               belv:UUIDConcept         .
    ?s        skos:inScheme          ?uuidURI                 .
    ?eq       rdf:type               belv:UUIDConcept         .
    ?eq       skos:inScheme          ?uuidURI                 .
    ?uuidURI  rdf:type               belv:UUIDConceptScheme   .
    ?uuidURI  rdf:type               skos:ConceptScheme       .
    ?uuidURI  rdf:type               belv:belv:UUIDConcept    .
}
WHERE {
    ?s        rdf:type               belv:NamespaceConcept    .
    FILTER NOT EXISTS {
        ?s    rdf:type               belv:UUIDConcept         .
    }
    BIND(URI(CONCAT("http://www.openbel.org/bel/uuid/", StrUUID())) AS ?uuidURI) .
    ?s        skos:exactMatch        ?eq                      .
    FILTER NOT EXISTS {
        ?eq   rdf:type               belv:UUIDConcept         .
    }
}

insert

PREFIX belv: <http://www.openbel.org/vocabulary/>
PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>

INSERT {
    ?s        rdf:type               belv:UUIDConcept         .
    ?s        skos:inScheme          ?uuidURI                 .
    ?eq       rdf:type               belv:UUIDConcept         .
    ?eq       skos:inScheme          ?uuidURI                 .
    ?uuidURI  rdf:type               belv:UUIDConceptScheme   .
    ?uuidURI  rdf:type               skos:ConceptScheme       .
    ?uuidURI  rdf:type               belv:belv:UUIDConcept    .
}
WHERE {
    ?s        rdf:type               belv:NamespaceConcept    .
    FILTER NOT EXISTS {
        ?s    rdf:type               belv:UUIDConcept         .
    }
    BIND(URI(CONCAT("http://www.openbel.org/bel/uuid/", StrUUID())) AS ?uuidURI) .
    ?s        skos:exactMatch        ?eq                      .
    FILTER NOT EXISTS {
        ?eq   rdf:type               belv:UUIDConcept         .
    }
}

UsingJena.java

package org.openbel.resource_reasoner;

import org.apache.jena.query.*;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ResIterator;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.update.UpdateAction;
import org.apache.jena.update.UpdateFactory;
import org.apache.jena.update.UpdateRequest;
import org.apache.jena.vocabulary.RDF;

import java.io.IOException;
import java.io.InputStream;
import java.util.Scanner;

import static org.openbel.resource_reasoner.RDFFunctions.createResource;
import static org.openbel.resource_reasoner.RDFFunctions.log;

public class UUID {

    public static final Resource BELV_NamespaceConcept = createResource("http://www.openbel.org/vocabulary/NamespaceConcept");

    public static void main(String[] args) throws IOException {
        Dataset ds = RDFFunctions.dataset_("rdf_db");

        InputStream sparqlInsert = Main.class.getResourceAsStream("/insert_uuid.sparql");
        String insertUUID = new Scanner(sparqlInsert, "UTF-8").useDelimiter("\\A").next();
        UpdateRequest req = UpdateFactory.create(insertUUID, Syntax.syntaxSPARQL_11);

        Model m = ds.getDefaultModel();
        ResIterator concepts = m.listSubjectsWithProperty(RDF.type, BELV_NamespaceConcept);
        long count = 0;
        while (concepts.hasNext()) {
            Resource concept = concepts.nextResource();
            QuerySolutionMap binding = new QuerySolutionMap();
            binding.add("s", concept);
            UpdateAction.execute(req, ds, binding);
            log("Created UUID cluster around %s", concept.toString());

            count += 1;
            if (count % 1000 == 0) {
                log("%s UUID clusters", count);
            }
        }
    }
}

uuid_cluster_count.sparql

SELECT (COUNT(?s) AS ?uuidCount)
WHERE {
    ?s a <http://www.openbel.org/vocabulary/UUIDConceptScheme> .
}

# Count is 157302.