A set of SPARQL examples that are used in different SIB resources
Proteins with no reported mitochondrial localization but interacting with 20 or more mitochondrial proteins ('gold' quality)
PREFIX : <http://nextprot.org/rdf/>
PREFIX nextprot_cv: <http://nextprot.org/rdf/terminology/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT DISTINCT ?entry (str(?gen) as ?gene) (count(distinct ?mitopartner) as ?mitcount) (count(distinct ?partner) as ?itcount) WHERE {
values ?mitloc {nextprot_cv:GO_0005739 nextprot_cv:SL-0173} # GO and SL values for mitochondrion
?entry :isoform ?iso.
?entry :gene / :recommendedName / rdfs:label ?gen.
filter not exists { ?iso :cellularComponent /:term / :childOf ?mitloc }
?iso :binaryInteraction ?it, ?it2.
?it :interactant ?mitopartner; :quality :GOLD .
?mitopartner :isoform / :cellularComponent ?loc .
?loc :quality :GOLD; :term / :childOf ?mitloc .
?it2 :interactant ?partner; :quality :GOLD .
} group by ?entry ?gen ?mitcnt having (count(distinct ?mitopartner) >= 20)
order by desc(?mitcnt)
graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
v11("?_anon_aaf95e3c346c4c97af230d5bcfeba8ab3110")
v4("?entry"):::projected
v5("?gen"):::projected
v12("?gene")
v2("?iso")
v6("?it")
v7("?it2")
v14("?itcount")
v9("?loc")
v1("?mitcnt")
v13("?mitcount")
v4("?mitloc")
v8("?mitopartner"):::projected
v10("?partner"):::projected
a4((" "))
a5((" "))
a2((" "))
a3((" "))
a6((" "))
a7((" "))
a1((" "))
c12([":GOLD"]):::iri
f0[[" >= '20^^xsd:integer'"]]
f0 --> a1
f1[["not "]]
subgraph f1e0["Exists Clause"]
e0v1 --":cellularComponent"--> e0a1
e0a1 --":term"--> e0a2
e0a2 --":childOf"--> e0v2
e0v1("?iso"):::projected
e0v2("?mitloc"):::projected
e0a1((" ")):::projected
e0a2((" ")):::projected
end
f1--EXISTS--> f1e0
f1 --> v2
f1 --> c2
f1 --> a2
f1 --> c3
f1 --> a3
f1 --> c4
f1 --> v4
v2 --":cellularComponent"--> a2
a2 --":term"--> a3
a3 --":childOf"--> v4
bind2[/VALUES ?mitloc/]
bind2-->v4
bind20([":terminology/GO_0005739"])
bind20 --> bind2
bind21([":terminology/SL-0173"])
bind21 --> bind2
v4 --":isoform"--> v2
v4 --":gene"--> a4
a4 --":recommendedName"--> a5
a5 --"rdfs:label"--> v5
v2 --":binaryInteraction"--> v6
v2 --":binaryInteraction"--> v7
v6 --":interactant"--> v8
v6 --":quality"--> c12
v8 --":isoform"--> a6
a6 --":cellularComponent"--> v9
v9 --":quality"--> c12
v9 --":term"--> a7
a7 --":childOf"--> v4
v7 --":interactant"--> v10
v7 --":quality"--> c12
bind6[/"count(?mitopartner)"/]
v8 --o bind6
bind6 --as--o v11
bind7[/"str(?gen)"/]
v5 --o bind7
bind7 --as--o v12
bind8[/"count(?mitopartner)"/]
v8 --o bind8
bind8 --as--o v13
bind9[/"count(?partner)"/]
v10 --o bind9
bind9 --as--o v14