Query

Query 1: Find the genes related to diabetes.

 select ?s1 ?o1 ?o2 
where{ 
?s1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>   <http://bio2rdf.org/omim_vocabulary:Gene>.
?s1   <http://bio2rdf.org/omim_vocabulary:refers-to> ?o1. 
?o1   <http://bio2rdf.org/omim_vocabulary:x-snomed> ?o2.
<http://bio2rdf.org/pharmgkb:PA446359> <http://bio2rdf.org/pharmgkb_vocabulary:x-snomedct> ?o2.
}

Query 2: find out all the drugs, which are substrate of some enzyme, their category and reaction.

PREFIX kegg: <http://bio2rdf.org/kegg_vocabulary:>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX drugbank: <http://bio2rdf.org/drugbank_vocabulary:>

SELECT * 
WHERE {  
?enzyme kegg::substrate ?cpd.
?enzyme <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/kegg_vocabulary:Enzyme>. 
?reaction kegg:enzyme  ?enzyme. 
?reaction kegg::reaction ?equation. 
?drug    drugbank::category ?category. 
?drug dcterms:description ?desc.
?drug drugbank:x-kegg ?cpd. 
 }

Query 3:

PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX sider:  <http://bio2rdf.org/sider:>
PREFIX sider_vocab: <http://bio2rdf.org/sider_vocabulary:>
PREFIX sider_resource: <http://bio2rdf.org/sider_resource:>
PREFIX drugbank: <http://bio2rdf.org/drugbank_vocabulary:>
PREFIX pubchem: <http://bio2rdf.org/pubchem.compound:>
PREFIX dbowl: <http://dbpedia.org/ontology/>

select *
where{

?drug sider_vocab:generic-name ?generic;
dcterms:title ?drug_name;
sider_vocab:side-effect ?side.
?drug sider_vocab:pubchem-flat-compound-id ?cpd.
?generic dcterms:title ?generic_name.
?side dcterms:title ?side_effect.

 ?drug_drugbank drugbank:category drugbank:Anti-Allergic-Agents.
 ?drug_drugbank drugbank:x-pubchemcompound ?cpd.
#  ?drug_drugbank drugbank:half-life ?halflife.
#   ?drug_drugbank drugbank:brand ?brand
#  ?drug_drugbank drugbank:product  ?product.

}

Query 4: Find the side effect and pathway of the anticonvulsants

PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX sider:  <http://bio2rdf.org/sider:>
PREFIX sider_vocab: <http://bio2rdf.org/sider_vocabulary:>
PREFIX sider_resource: <http://bio2rdf.org/sider_resource:>
PREFIX drugbank: <http://bio2rdf.org/drugbank_vocabulary:>
PREFIX pubchem: <http://bio2rdf.org/pubchem.compound:>
PREFIX dbowl: <http://dbpedia.org/ontology/>
PREFIX kegg: <http://bio2rdf.org/kegg_vocabulary:>

select *
where{

 ?drug_drugbank drugbank:category drugbank:Anticonvulsants.
 ?drug_drugbank drugbank:affected-organism ?affected.
 ?drug_drugbank drugbank:x-pubchemcompound ?cpd.

?drug sider_vocab:side-effect ?side.
?drug sider_vocab:pubchem-flat-compound-id ?cpd.
?side dcterms:title ?side_effect.

?drug_kegg kegg:x-pubchem.compound ?cpd.
 ?drug_kegg kegg:pathway  ?pathway.}