Example #1
0
  public String getWikiPageRedirectsQuery(String subject) throws Exception {
    ISparqlQuery query = SparqlQueryManager.getInstance().createQuery();
    QueryUtil.getInstance()
        .getCommonPrefixes(query)
        .addSelectParamaters(true, "?page")
        .addTriplePattern("<" + subject + ">", "rdf:type", "dbpedia-owl:Drug")
        .addTriplePattern("?page", "dbpedia-owl:wikiPageRedirects", "<" + subject + ">");

    return query.buildQueryString();
  }
Example #2
0
  public String getCreateIndexFileQuery() throws Exception {
    ISparqlQuery query = SparqlQueryManager.getInstance().createQuery();
    QueryUtil.getInstance()
        .getCommonPrefixes(query)
        .addSelectParamaters(true, "?s", "?label", "?drugbankID", "?casNumber")
        .addFiltredTriplePattern(
            "?s", "rdfs:label", "?label", new LangFilterElement("?label", ISparqlQuery.LANG_EN))
        .addOptionalPattern(new TriplePatternElement("?s", "dbpprop:drugbank", "?drugbankID"))
        .addOptionalPattern(new TriplePatternElement("?s", "dbpedia-owl:casNumber", "?casNumber"))
        .addGroupGraphPattern(new TriplePatternElement("?s", "rdf:type", "dbpedia-owl:Drug"))
        .addUnionPattern(
            new TriplePatternElement("?s", "rdf:type", "dbpedia-owl:ChemicalCompound"));

    return query.buildQueryString();
  }
Example #3
0
  public String getDBPediaDataQuery(String drugName) throws Exception {
    ISparqlQuery query = SparqlQueryManager.getInstance().createQuery();

    QueryUtil.getInstance()
        .getCommonPrefixes(query)
        .addSelectParamaters(true, "?abstract", "?wikiPage", "?drugbankID")
        .addTriplePattern("?s", "rdfs:label", "\"" + drugName + "\"@en")
        .addFiltredTriplePattern(
            "?s",
            "dbpedia-owl:abstract",
            "?abstract",
            new LangFilterElement("?abstract", ISparqlQuery.LANG_EN))
        .addOptionalPattern(new TriplePatternElement("?s", "foaf:isPrimaryTopicOf", "?wikiPage"))
        .addOptionalPattern(
            new TriplePatternElement(
                "?s",
                "owl:sameAs",
                "?drugbankID",
                new FilterElement("regex(str(?drugbankID),\"drugbank\",\"i\")")));

    return query.buildQueryString();
  }
Example #4
0
  public String getDrugbankEnzymesQuery(String subject) throws Exception {
    ISparqlQuery query = SparqlQueryManager.getInstance().createQuery();
    QueryUtil.getInstance()
        .getCommonPrefixes(query)
        .addSelectParamaters(
            true, "?cellularLoc", "?reaction", "?specificFunction", "?molWeight", "?theoPi")
        .addOptionalPattern(
            new TriplePatternElement(
                "<" + subject + ">", "drugbankvoca:cellular-location", "?cellularLoc"))
        .addOptionalPattern(
            new TriplePatternElement("<" + subject + ">", "drugbankvoca:reaction", "?reaction"))
        .addOptionalPattern(
            new TriplePatternElement(
                "<" + subject + ">", "drugbankvoca:specific-function", "?specificFunction"))
        .addOptionalPattern(
            new TriplePatternElement(
                "<" + subject + ">", "drugbankvoca:molecular-weight", "?molWeight"))
        .addOptionalPattern(
            new TriplePatternElement(
                "<" + subject + ">", "drugbankvoca:theoretical-pi", "?theoPi"));

    return query.buildQueryString();
  }
Example #5
0
  public String getDrugbankQuery(Drugbank drugbank) throws Exception {

    if (drugbank.getDrugbankID() != null) {

      ISparqlQuery query = SparqlQueryManager.getInstance().createQuery();
      QueryUtil.getInstance()
          .getCommonPrefixes(query)
          .addSelectParamaters(
              true,
              "?description",
              "?synonym",
              "?link",
              "?absorption",
              "?clearance",
              "?roe",
              "?vod",
              "?halfLife",
              "?enzyme",
              "?enzymeName");
      query
          .addTriplePattern(
              "drugbankbio:" + drugbank.getDrugbankID(), "dc:description", "?description")
          .addOptionalPattern(
              new TriplePatternElement(
                  "drugbankbio:" + drugbank.getDrugbankID(), "drugbankvoca:synonym", "?synonym"))
          .addOptionalPattern(
              new TriplePatternElement(
                  "drugbankbio:" + drugbank.getDrugbankID(), "rdfs:seeAlso", "?link"))
          .addOptionalPattern(
              new TriplePatternElement(
                  "drugbankbio:" + drugbank.getDrugbankID(),
                  "drugbankvoca:route-of-elimination",
                  "?roe"))
          .addOptionalPattern(
              new TriplePatternElement(
                  "drugbankbio:" + drugbank.getDrugbankID(),
                  "drugbankvoca:volume-of-distribution",
                  "?vod"))
          .addOptionalPattern(
              new TriplePatternElement(
                  "drugbankbio:" + drugbank.getDrugbankID(), "drugbankvoca:half-life", "?halfLife"))
          .addOptionalPattern(
              new TriplePatternElement(
                  "drugbankbio:" + drugbank.getDrugbankID(), "drugbankvoca:enzyme", "?enzyme"),
              new TriplePatternElement("?enzyme", "drugbankvoca:name", "?enzymeName"))
          .addOptionalPattern(
              new TriplePatternElement(
                  "drugbankbio:" + drugbank.getDrugbankID(),
                  "drugbankvoca:clearance",
                  "?clearance"))
          .addOptionalPattern(
              new TriplePatternElement(
                  "drugbankbio:" + drugbank.getDrugbankID(),
                  "drugbankvoca:absorption",
                  "?absorption"));

      return query.buildQueryString();
    }

    ISparqlQuery query = SparqlQueryManager.getInstance().createQuery();
    QueryUtil.getInstance()
        .getCommonPrefixes(query)
        .addSelectParamaters(
            true,
            "?description",
            "?synonym",
            "?link",
            "?absorption",
            "?clearance",
            "?roe",
            "?vod",
            "?halfLife");
    query
        .addTriplePattern("?s", "dc:description", "?description")
        .addOptionalPattern(new TriplePatternElement("?s", "drugbankvoca:synonym", "?synonym"))
        .addOptionalPattern(new TriplePatternElement("?s", "rdfs:seeAlso", "?link"))
        .addOptionalPattern(new TriplePatternElement("?s", "drugbankvoca:clearance", "?clearance"))
        .addOptionalPattern(
            new TriplePatternElement("?s", "drugbankvoca:route-of-elimination", "?roe"))
        .addOptionalPattern(new TriplePatternElement("?s", "drugbankvoca:half-life", "?halfLife"))
        .addOptionalPattern(
            new TriplePatternElement("?s", "drugbankvoca:volume-of-distribution", "?vod"))
        .addOptionalPattern(
            new TriplePatternElement("?s", "drugbankvoca:absorption", "?absorption"))
        .addGroupGraphPattern(
            new TriplePatternElement(
                "?s", "drugbankvoca:xref", "bioCas:" + drugbank.getCasNumber()));

    return query.buildQueryString();
  }
Example #6
0
  public String getDrugbank2Query(Drugbank drugbank) throws Exception {

    if (drugbank.getDrugbankID() != null) {
      ISparqlQuery query = SparqlQueryManager.getInstance().createQuery();
      QueryUtil.getInstance()
          .getCommonPrefixes(query)
          .addSelectParamaters(
              true,
              "?description",
              "?synonym",
              "?absorption",
              "?clearance",
              "?molWeightMono",
              "?molWeightAvg",
              "?halfLife");
      query
          .addTriplePattern(
              "drugs:" + drugbank.getDrugbankID(), "drugbank:description", "?description")
          .addOptionalPattern(
              new TriplePatternElement(
                  "drugs:" + drugbank.getDrugbankID(), "drugbank:synonym", "?synonym"))
          .addOptionalPattern(
              new TriplePatternElement(
                  "drugs:" + drugbank.getDrugbankID(), "drugbank:absorption", "?absorption"))
          .addOptionalPattern(
              new TriplePatternElement(
                  "drugs:" + drugbank.getDrugbankID(),
                  "drugbank:molecularWeightMono",
                  "?molWeightMono"))
          .addOptionalPattern(
              new TriplePatternElement(
                  "drugs:" + drugbank.getDrugbankID(),
                  "drugbank:molecularWeightAverage",
                  "?molWeightAvg"))
          .addOptionalPattern(
              new TriplePatternElement(
                  "drugs:" + drugbank.getDrugbankID(), "drugbank:halfLife", "?halfLife"))
          .addOptionalPattern(
              new TriplePatternElement(
                  "drugs:" + drugbank.getDrugbankID(), "drugbank:clearance", "?clearance"));

      return query.buildQueryString();
    }

    ISparqlQuery query2 = SparqlQueryManager.getInstance().createQuery();
    QueryUtil.getInstance()
        .getCommonPrefixes(query2)
        .addSelectParamaters(
            true, "?description", "?synonym", "?absorption", "?clearance", "?molWeightAvg");
    query2
        .addTriplePattern("?s", "drugbank:description", "?description")
        .addOptionalPattern(new TriplePatternElement("?s", "drugbank:synonym", "?synonym"))
        .addOptionalPattern(new TriplePatternElement("?s", "drugbank:absorption", "?absorption"))
        .addOptionalPattern(new TriplePatternElement("?s", "drugbank:clearance", "?clearance"))
        .addOptionalPattern(
            new TriplePatternElement("?s", "drugbank:molecularWeightMono", "?molWeightMono"))
        .addOptionalPattern(
            new TriplePatternElement("?s", "drugbank:molecularWeightAverage", "?molWeightAvg"))
        .addOptionalPattern(new TriplePatternElement("?s", "drugbank:halfLife", "?halfLife"))
        .addGroupGraphPattern(
            new TriplePatternElement(
                "?s", "drugbank:casRegistryNumber", "bioCas:" + drugbank.getCasNumber()))
        .addUnionPattern(
            new TriplePatternElement("?s", "rdfs:label", "\"" + drugbank.getDrugName() + "\""));

    return query2.buildQueryString();
  }