Data

Dataset	#triples	#subjects	#predicates	#objects	#types
omim	8,750,774	1,013,389	101	1,415,364	34
pharmgkb	278,049,209	25,325,504	88	25,684,235	50
drugbank	3,649,750	316,555	105	369,947	91
sider	17,627,864	1,222,429	39	648,555	16
kegg	50,197,150	6,533,307	141	6,792,319	63

Query

Query	#triplePattern	#Result
q1	4	5
q2	9	40
q3	7	790
q4	8	9492
q5	8	111962

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 the articles about GPA patients and its drug functions,clinical features.

SELECT *
WHERE {
?s <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/omim_vocabulary:Phenotype> .
?s <http://www.w3.org/2000/01/rdf-schema#label> ?o.
?s <http://bio2rdf.org/omim_vocabulary:clinical-features> ?clinicFeature.
?s <http://bio2rdf.org/omim_vocabulary:article> ?article.
?s <http://bio2rdf.org/omim_vocabulary:x-uniprot> ?protein.
filter(regex(str(?o),"GLUCOCORTICOID-REMEDIABLE ALDOSTERONISM","i"))
?drug  <http://bio2rdf.org/drugbank_vocabulary:gene-name> ?geneName.
 ?drug <http://bio2rdf.org/drugbank_vocabulary:x-uniprot> ?protein.
?drug  <http://bio2rdf.org/drugbank_vocabulary:general-function> ?genFunction.
?drug  <http://bio2rdf.org/drugbank_vocabulary:specific-function> ?speFunction.

}

Query 3: 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 3s:

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. 
 } limit 100

Query 4:

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 5: 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.}

Query 5s:

add "limit 100" clause to Query 5.

Rewritten query with "service" keyword:

Query 1:

Query 1':

select ?s1 ?o1 ?o2 
where{
service<http://omim.bio2rdf.org/sparql>
{
?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.}

service<http://pharmgkb.bio2rdf.org/sparql>
{<http://bio2rdf.org/pharmgkb:PA446359> <http://bio2rdf.org/pharmgkb_vocabulary:x-snomedct> ?o2.}
} 

Query 1":

select ?s1 ?o1 ?o2 
where{
service<http://omim.bio2rdf.org/sparql>
{
?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.}

service<http://pharmgkb.bio2rdf.org/sparql>
{<http://bio2rdf.org/pharmgkb:PA446359> <http://bio2rdf.org/pharmgkb_vocabulary:x-snomedct> ?o2.}

} 

Query 2':

SELECT *
WHERE {
service<http://cu.omim.bio2rdf.org/sparql>{
?s <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/omim_vocabulary:Phenotype> .
?s <http://www.w3.org/2000/01/rdf-schema#label> ?o.
?s <http://bio2rdf.org/omim_vocabulary:clinical-features> ?clinicFeature.
?s <http://bio2rdf.org/omim_vocabulary:article> ?article.
?s <http://bio2rdf.org/omim_vocabulary:x-uniprot> ?protein.
filter(regex(str(?o),"GLUCOCORTICOID-REMEDIABLE ALDOSTERONISM","i"))}

service<http://cu.drugbank.bio2rdf.org/sparql>

 {
?drug  <http://bio2rdf.org/drugbank_vocabulary:gene-name> ?geneName.
 ?drug <http://bio2rdf.org/drugbank_vocabulary:x-uniprot> ?protein.
?drug  <http://bio2rdf.org/drugbank_vocabulary:general-function> ?genFunction.
?drug  <http://bio2rdf.org/drugbank_vocabulary:specific-function> ?speFunction.

}
}

Query 2":

SELECT *
WHERE {


service<http://cu.drugbank.bio2rdf.org/sparql>

 {
?drug  <http://bio2rdf.org/drugbank_vocabulary:gene-name> ?geneName.
 ?drug <http://bio2rdf.org/drugbank_vocabulary:x-uniprot> ?protein.
?drug  <http://bio2rdf.org/drugbank_vocabulary:general-function> ?genFunction.
?drug  <http://bio2rdf.org/drugbank_vocabulary:specific-function> ?speFunction.

}
service<http://cu.omim.bio2rdf.org/sparql>{
?s <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/omim_vocabulary:Phenotype> .
?s <http://www.w3.org/2000/01/rdf-schema#label> ?o.
?s <http://bio2rdf.org/omim_vocabulary:clinical-features> ?clinicFeature.
?s <http://bio2rdf.org/omim_vocabulary:article> ?article.
?s <http://bio2rdf.org/omim_vocabulary:x-uniprot> ?protein.
filter(regex(str(?o),"GLUCOCORTICOID-REMEDIABLE ALDOSTERONISM","i"))}
}

Query 3':

SELECT *
WHERE {
service<http://cu.kegg.bio2rdf.org/sparql>
{
 ?enzyme <http://bio2rdf.org/kegg_vocabulary:substrate> ?cpd.
  ?enzyme rdf:type <http://bio2rdf.org/kegg_vocabulary:Enzyme>.
 ?reaction <http://bio2rdf.org/kegg_vocabulary:enzyme>  ?enzyme. 
  ?reaction <http://bio2rdf.org/kegg_vocabulary:reaction> ?equation.
}
service<http://cu.drugbank.bio2rdf.org/sparql>
{
 ?drug <http://bio2rdf.org/drugbank_vocabulary:category> ?cat.
 ?drug <http://purl.org/dc/terms/description> ?desc.
?drug <http://bio2rdf.org/drugbank_vocabulary:x-kegg> ?cpd
  }
  }

Query 3": exchange the order of two service clauses in the query 3'.

Query 4':

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 bio2rdf: <http://bio2rdf.org/bio2rdf_vocabulary:>
PREFIX pubchem: <http://bio2rdf.org/pubchem.compound:>
PREFIX dbowl: <http://dbpedia.org/ontology/>

select *
where { service<http://cu.sider.bio2rdf.org/sparql>

{
?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.}

service<http://cu.drugbank.bio2rdf.org/sparql>
{
 ?drug2 <http://bio2rdf.org/drugbank_vocabulary:category> <http://bio2rdf.org/drugbank_vocabulary:Anti-Allergic-Agents>.
 ?drug2 <http://bio2rdf.org/drugbank_vocabulary:x-pubchemcompound> ?cpd.

}

}

Query 4": exchange the order of two service clauses in the query 4'.

Query 5':

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{
service<http://cu.drugbank.bio2rdf.org/sparql>{
 ?drug_drugbank drugbank:category drugbank:Anticonvulsants.
 ?drug_drugbank drugbank:affected-organism ?affected.
 ?drug_drugbank drugbank:x-pubchemcompound ?cpd.}

service<http://cu.kegg.bio2rdf.org/sparql>
 {?drug_kegg kegg:x-pubchem.compound ?cpd.
 ?drug_kegg kegg:pathway  ?pathway.}

service<http://cu.sider.bio2rdf.org/sparql>
{
?drug sider_vocab:side-effect ?side.
?side dcterms:title ?side_effect.
?drug sider_vocab:pubchem-flat-compound-id ?cpd.}
}

Query 5": Change the order of the first two service clauses in the query 5'.