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README.md

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----
-license: mit
----
+# sparql-api
+SPARQL queries for use with grlc

drugbank-drug-goa.rq

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+#+ summary: We should add a summary.
+#+ endpoint: "http://example.com/sparql"
+
+PREFIX dct: <http://purl.org/dc/terms/>
+PREFIX dv: <http://bio2rdf.org/drugbank_vocabulary:>
+PREFIX hv: <http://bio2rdf.org/hgnc_vocabulary:>
+PREFIX goa: <http://bio2rdf.org/goa_vocabulary:>
+PREFIX kv: <http://bio2rdf.org/kegg_vocabulary:>
+
+SELECT distinct ?drugid ?g
+{
+?drug <http://bio2rdf.org/openpredict_vocabulary:indication> ?disease .
+{
+?drug a dv:Drug .
+?drug dv:target ?t .
+?t dv:x-hgnc ?x .
+}
+UNION {
+?d a kv:Drug .
+?d kv:target ?l .
+?l kv:link ?t .
+BIND (URI( REPLACE(str(?t),"HSA","hsa")) AS ?target) .
+?target a kv:Gene .
+?target kv:x-hgnc ?x .
+?d kv:x-drugbank ?drug .
+}
+?x hv:x-uniprot ?uniprot .
+?uniprot ?p ?go .
+FILTER (?p = goa:process || ?p = goa:component || ?p = goa:function)
+BIND(STRAFTER(str(?go),  "http://bio2rdf.org/") AS $g)
+BIND ( STRAFTER(str(?drug),"http://bio2rdf.org/drugbank:") AS ?drugid)
+}

drugbank-drug-smiles.rq

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+#+ summary: We should add a summary.
+#+ endpoint: "http://example.com/sparql"
+
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX dv: <http://bio2rdf.org/drugbank_vocabulary:>
+PREFIX sv: <http://bio2rdf.org/sider_vocabulary:>
+
+SELECT distinct ?drugid ?smiles
+{
+ ?d <http://bio2rdf.org/openpredict_vocabulary:indication> ?disease .
+ ?d a dv:Drug .
+ ?d dv:calculated-properties ?cp .
+ ?cp a dv:SMILES .
+ ?cp dv:value ?smiles .
+ BIND( STRAFTER(str(?d), "http://bio2rdf.org/drugbank:") AS ?drugid)
+}

drugbank-drug-synonym.rq

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+PREFIX dv: <http://bio2rdf.org/drugbank_vocabulary:>
+PREFIX dc: <http://purl.org/dc/terms/>
+select ?drugid ?name where { 
+	?d ?p dv:Drug .
+    {
+    ?d dv:synonym ?s .
+    ?s dc:title ?name .
+	}
+    UNION
+    {
+    ?d dc:title ?name
+	}
+    BIND ( STRAFTER(str(?d),"http://bio2rdf.org/drugbank:") AS ?drugid)
+} 

drugbank-drug-target.rq

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+#+ summary: We should add a summary.
+#+ endpoint: "http://example.com/sparql"
+
+PREFIX iv: <http://bio2rdf.org/irefindex_vocabulary:>
+PREFIX dv: <http://bio2rdf.org/drugbank_vocabulary:>
+PREFIX hv: <http://bio2rdf.org/hgnc_vocabulary:>
+PREFIX kv: <http://bio2rdf.org/kegg_vocabulary:>
+SELECT DISTINCT ?drugid ?geneid WHERE {
+?drug <http://bio2rdf.org/openpredict_vocabulary:indication> ?disease .
+{
+?d a kv:Drug .
+?d kv:target ?l .
+?l kv:link ?t .
+BIND (URI( REPLACE(str(?t),"HSA","hsa")) AS ?target) .
+?target a kv:Gene .
+?target kv:x-ncbigene ?ncbi .
+?d kv:x-drugbank ?drug .
+}
+UNION
+{
+  ?drug a dv:Drug .
+  ?drug dv:target ?target .
+  ?target dv:x-hgnc ?hgnc .
+  ?hgnc hv:x-ncbigene ?ncbi .
+}
+BIND ( STRAFTER(str(?ncbi),"http://bio2rdf.org/ncbigene:") AS ?geneid)
+BIND ( STRAFTER(str(?drug),"http://bio2rdf.org/drugbank:") AS ?drugid)
+
+}

drugbank-sider-sideeffects.rq

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+#+ summary: We should add a summary.
+#+ endpoint: "http://example.com/sparql"
+
+PREFIX dv: <http://bio2rdf.org/drugbank_vocabulary:>
+PREFIX ov: <http://bio2rdf.org/openpredict_vocabulary:>
+PREFIX sider: <http://bio2rdf.org/sider_vocabulary:>
+
+SELECT distinct ?drugid ?umlsid
+{
+?dia sider:drug ?stitch_flat .
+?dia sider:effect ?se .
+{
+?stitch_flat sider:x-pubchem.compound ?pc .
+}
+UNION{
+?stitch_flat sider:stitch-stereo ?stitch_stereo .
+?stitch_stereo sider:x-pubchem.compound ?pc .
+}
+{
+?d ov:x-pubchemcompound ?pc  .
+}
+UNION 
+{
+?d dv:x-pubchemcompound ?pc  .       
+}
+?d ov:indication ?disease .     
+BIND(STRAFTER( str(?d), "http://bio2rdf.org/drugbank:") AS ?drugid) 
+BIND(STRAFTER( str(?se), "http://bio2rdf.org/umls:") AS ?umlsid)
+}

drugbank-target-seq.rq

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+#+ summary: We should add a summary.
+#+ endpoint: "http://example.com/sparql"
+
+PREFIX dv: <http://bio2rdf.org/drugbank_vocabulary:>
+PREFIX hv: <http://bio2rdf.org/hgnc_vocabulary:>
+PREFIX sider: <http://bio2rdf.org/sider_vocabulary:>
+
+SELECT distinct ?geneid ?seq
+{
+  ?drug <http://bio2rdf.org/openpredict_vocabulary:indication> ?disease .
+  ?d a dv:Drug .
+  ?d dv:target ?t .
+  #?t a dv:Target .
+  ?t dv:x-hgnc ?hgnc .
+  ?hgnc hv:x-ncbigene ?ncbi .
+  ?t dv:amino-acid-sequence ?seq .
+BIND ( STRAFTER(str(?ncbi),"http://bio2rdf.org/ncbigene:") AS ?geneid)
+}

human-interactome.rq

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+#+ summary: We should add a summary.
+#+ endpoint: "http://example.com/sparql"
+
+PREFIX iv: <http://bio2rdf.org/irefindex_vocabulary:>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+SELECT distinct ?geneid1 ?geneid2
+WHERE {
+   ?s rdf:type <http://edamontology.org/topic_0128> .
+   ?s iv:interactor_a ?gene1 .
+   ?s iv:interactor_b ?gene2  .
+    BIND(STRAFTER( str(?gene1), "http://bio2rdf.org/ncbigene:") AS ?geneid1) 
+    BIND(STRAFTER( str(?gene2), "http://bio2rdf.org/ncbigene:") AS ?geneid2) 
+}

omim-disease-hpo.rq

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+#+ summary: We should add a summary.
+#+ endpoint: "http://example.com/sparql"
+ PREFIX ov: <http://bio2rdf.org/openpredict_vocabulary:>
+ PREFIX dct: <http://purl.org/dc/terms/>
+ SELECT distinct ?diseaseid ?hpoid
+ WHERE{
+    ?drug ov:indication ?disease .
+    GRAPH <http://w3id.org/fairworkflows/dataset.openpredict.hpoannot.R1>{
+    ?disease <http://semanticscience.org/resource/SIO_000255> ?hpo .
+    BIND( STRAFTER(str(?disease),"http://bio2rdf.org/omim:") AS ?diseaseid)
+    BIND( STRAFTER(str(?hpo),"http://bio2rdf.org/") AS ?hpoid)
+}
+}

omim-disease-mesh-bioportal.rq

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+#+ summary: We should add a summary.
+#+ endpoint: "http://example.com/sparql"
+ 
+ PREFIX ov: <http://bio2rdf.org/openpredict_vocabulary:>
+ PREFIX dct: <http://purl.org/dc/terms/>
+ SELECT distinct ?diseaseid ?hpoid
+ WHERE{
+    ?drug ov:indication ?disease .
+    GRAPH <http://w3id.org/fairworkflows/dataset.openpredict.meshannot_bioportal.R1>
+    {
+    ?disease <http://semanticscience.org/resource/SIO_000255> ?hpo .
+    BIND( STRAFTER(str(?disease),"http://bio2rdf.org/omim:") AS ?diseaseid)
+    BIND( STRAFTER(str(?hpo),"http://bio2rdf.org/") AS ?hpoid)
+}
+}

omim-disease-mesh.rq

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+#+ summary: We should add a summary.
+#+ endpoint: "http://example.com/sparql"
+ 
+ PREFIX ov: <http://bio2rdf.org/openpredict_vocabulary:>
+ PREFIX dct: <http://purl.org/dc/terms/>
+ SELECT distinct ?diseaseid ?hpoid
+ WHERE{
+    ?drug ov:indication ?disease .
+    GRAPH <http://w3id.org/fairworkflows/dataset.openpredict.meshannot.R1>
+    {
+    ?disease <http://semanticscience.org/resource/SIO_000255> ?hpo .
+    BIND( STRAFTER(str(?disease),"http://bio2rdf.org/omim:") AS ?diseaseid)
+    BIND( STRAFTER(str(?hpo),"http://bio2rdf.org/") AS ?hpoid)
+}
+}

openpredict-omim-drug.rq

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+#+ summary: We should add a summary.
+#+ endpoint: "http://example.com/sparql"
+
+ PREFIX ov: <http://bio2rdf.org/openpredict_vocabulary:>
+ SELECT distinct ?drugid ?omimid
+ {
+  ?drug ov:indication ?disease .
+  BIND( STRAFTER(str(?disease),"http://bio2rdf.org/omim:") AS ?omimid)
+  BIND( STRAFTER(str(?drug),"http://bio2rdf.org/drugbank:") AS ?drugid)
+
+}