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 |
q3s | 7 | 100 |
q5s | 8 | 100 |
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. ?drug dcterms:title ?drug_name . ?drug 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://cu.pharmgkb.bio2rdf.org/sparql> {<http://bio2rdf.org/pharmgkb:PA446359> <http://bio2rdf.org/pharmgkb_vocabulary:x-snomedct> ?o2.} service<http://cu.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.} }
Query 1":
select ?s1 ?o1 ?o2 where{ service<http://cu.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://cu.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'.