55

rq turtle/ttl

• binding site
• evidence tag
• count

Number of proteins with binding sites for metals or metal sulfur clusters (and experimental evidence for the binding)

Use at

• https://sparql.uniprot.org/sparql/

PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX up: <http://purl.uniprot.org/core/>

SELECT
  ?ligand
  ?ligandName 
  (COUNT(DISTINCT ?protein) as ?entries)
WHERE {
   ?protein up:annotation ?annotation .
   
   VALUES ?evs { obo:ECO_0000269 obo:ECO_0007744 } .
   VALUES ?chebids { CHEBI:25213 CHEBI:25214 } .
   ?st rdf:subject ?protein ; 
       rdf:predicate up:annotation ; 
       rdf:object ?annotation ;
       up:attribution/up:evidence ?evs .

   ?annotation up:ligand/rdfs:subClassOf ?ligand .
   ?ligand rdfs:subClassOf+ ?chebids ;
     rdfs:label ?ligandName .
}
GROUP BY ?ligand ?ligandName
ORDER BY DESC(?entries)

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v3("?annotation")
  v5("?chebids")
  v9("?entries")
  v4("?evs")
  v7("?ligand"):::projected 
  v8("?ligandName"):::projected 
  v2("?protein"):::projected 
  v6("?st")
  a1((" "))
  a2((" "))
  c1(["up:annotation"]):::iri 
  v2 -->c1--> v3
  bind0[/VALUES ?evs/]
  bind0-->v4
  bind00(["obo:ECO_0000269"])
  bind00 --> bind0
  bind01(["obo:ECO_0007744"])
  bind01 --> bind0
  bind1[/VALUES ?chebids/]
  bind1-->v5
  bind10(["obo:CHEBI_25213"])
  bind10 --> bind1
  bind11(["obo:CHEBI_25214"])
  bind11 --> bind1
  v6 --"rdf:subject"-->  v2
  v6 --"rdf:predicate"-->  c1
  v6 --"rdf:object"-->  v3
  v6 --"up:attribution"-->  a1
  a1 --"up:evidence"-->  v4
  v3 --"up:ligand"-->  a2
  a2 --"rdfs:subClassOf"-->  v7
  v7 --"rdfs:subClassOf"-->  v5
  v7 --"rdfs:label"-->  v8
  bind3[/"count(?protein)"/]
  v2 --o bind3
  bind3 --as--o v9