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();
}
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();
}
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();
}
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();
}
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();
}
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();
}