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138_unique_taxons_having_an_experimental_chebi

rq turtle/ttl

• ChEBI
• catalytic
• cofactor
• enzyme
• ligand

Count distinct taxons linked to ChEBI in different ways via experimental annotations in UniProt

Use at

• https://sparql.uniprot.org/sparql

PREFIX ECO: <http://purl.obolibrary.org/obo/ECO_>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX up: <http://purl.uniprot.org/core/>
SELECT 
  (COUNT(DISTINCT ?taxon) AS ?taxonsLinkedToChebi)
  (COUNT(DISTINCT ?ligandTaxon) AS ?taxonsLinkedToChebiViaLigand)
  (COUNT(DISTINCT ?cofactorTaxon) AS ?taxonsLinkedToChebiViaCofactor)
  (COUNT(DISTINCT ?catalyticTaxon) AS ?taxonsLinkedToChebiViaCatalytic)
WHERE {
  {
    GRAPH <http://sparql.uniprot.org/uniprot> {
      ?protein up:annotation ?ligandAnnotation .
      ?ligandAnnotation up:ligand/rdfs:subClassOf ?chebi .
      ?reif rdf:subject ?protein ; 
            rdf:object ?ligandAnnotation .
    }
  } UNION {
    GRAPH <http://sparql.uniprot.org/uniprot> {
      ?protein up:annotation ?cofactorAnnotation .
      ?cofactorAnnotation up:cofactor ?chebi .
      ?reif rdf:subject ?cofactorAnnotation ; 
            rdf:object ?chebi .
    }
  } UNION {
    GRAPH <http://sparql.uniprot.org/uniprot> {
      ?protein up:annotation ?catalyticActivityAnnotation .
      ?catalyticActivityAnnotation a up:Catalytic_Activity_Annotation ;
                                   up:catalyticActivity ?catalyticActivity .
      ?catalyticActivity up:catalyzedReaction ?rhea .
      ?reif rdf:subject ?catalyticActivityAnnotation ; 
            rdf:object ?catalyticActivity .
    }
    GRAPH <https://sparql.rhea-db.org/rhea> {
      ?rhea rh:side/rh:contains/rh:compound ?compound .
      ?compound (rh:chebi|(rh:reactivePart/rh:chebi)|rh:underlyingChebi) ?chebi .
    }     
  }
  GRAPH <http://sparql.uniprot.org/uniprot> {
    ?reif up:attribution ?attr .
    ?attr up:evidence ECO:0000269 .
    ?protein up:organism ?taxon .
    BIND(IF(BOUND(?ligandAnnotation),?taxon, ?_) AS ?ligandTaxon)
    BIND(IF(BOUND(?cofactorAnnotation),?taxon, ?_) AS ?cofactorTaxon)
    BIND(IF(BOUND(?catalyticActivityAnnotation),?taxon, ?_) AS ?catalyticTaxon)
  }
  GRAPH <http://sparql.uniprot.org/chebi> {
    ?chebi a owl:Class .
  }
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v10("?attr")
  v7("?catalyticActivity")
  v6("?catalyticActivityAnnotation")
  v14("?catalyticTaxon"):::projected 
  v3("?chebi")
  v5("?cofactorAnnotation")
  v13("?cofactorTaxon"):::projected 
  v9("?compound")
  v2("?ligandAnnotation")
  v12("?ligandTaxon"):::projected 
  v1("?protein")
  v4("?reif")
  v8("?rhea")
  v11("?taxon"):::projected 
  v15("?taxonsLinkedToChebi")
  v18("?taxonsLinkedToChebiViaCatalytic")
  v17("?taxonsLinkedToChebiViaCofactor")
  v16("?taxonsLinkedToChebiViaLigand")
  a2((" "))
  a3((" "))
  a1((" "))
  a4((" "))
  c23(["owl:Class"]):::iri 
  c21(["ECO:0000269"]):::iri 
  c9(["up:Catalytic_Activity_Annotation"]):::iri 
  subgraph union0[" Union "]
  subgraph union0l[" "]
    style union0l fill:#abf,stroke-dasharray: 3 3;
    subgraph union1[" Union "]
    subgraph union1l[" "]
      style union1l fill:#abf,stroke-dasharray: 3 3;
      v1 --"up:annotation"-->  v6
      v6 --"a"-->  c9
      v6 --"up:catalyticActivity"-->  v7
      v7 --"up:catalyzedReaction"-->  v8
      v4 --"rdf:subject"-->  v6
      v4 --"rdf:object"-->  v7
      v8 --"rh:side"-->  a2
      a2 --"rh:contains"-->  a3
      a3 --"rh:compound"-->  v9
      subgraph union2[" Union "]
      subgraph union2l[" "]
        style union2l fill:#abf,stroke-dasharray: 3 3;
        subgraph union3[" Union "]
        subgraph union3l[" "]
          style union3l fill:#abf,stroke-dasharray: 3 3;
          v9 --"rh:underlyingChebi"-->  v3
        end
        subgraph union3r[" "]
          style union3r fill:#abf,stroke-dasharray: 3 3;
          v9 --"rh:reactivePart"-->  a4
          a4 --"rh:chebi"-->  v3
        end
        union3r <== or ==> union3l
        end
      end
      subgraph union2r[" "]
        style union2r fill:#abf,stroke-dasharray: 3 3;
        v9 --"rh:chebi"-->  v3
      end
      union2r <== or ==> union2l
      end
    end
    subgraph union1r[" "]
      style union1r fill:#abf,stroke-dasharray: 3 3;
      v1 --"up:annotation"-->  v5
      v5 --"up:cofactor"-->  v3
      v4 --"rdf:subject"-->  v5
      v4 --"rdf:object"-->  v3
    end
    union1r <== or ==> union1l
    end
  end
  subgraph union0r[" "]
    style union0r fill:#abf,stroke-dasharray: 3 3;
    v1 --"up:annotation"-->  v2
    v2 --"up:ligand"-->  a1
    a1 --"rdfs:subClassOf"-->  v3
    v4 --"rdf:subject"-->  v1
    v4 --"rdf:object"-->  v2
  end
  union0r <== or ==> union0l
  end
  v4 --"up:attribution"-->  v10
  v10 --"up:evidence"-->  c21
  v1 --"up:organism"-->  v11
  bind0[/"if(bound(?ligandAnnotation),?taxon,?_)"/]
  v2 --o bind0
  v11 --o bind0
  null --o bind0
  bind0 --as--o v12
  bind1[/"if(bound(?cofactorAnnotation),?taxon,?_)"/]
  v5 --o bind1
  v11 --o bind1
  null --o bind1
  bind1 --as--o v13
  bind2[/"if(bound(?catalyticActivityAnnotation),?taxon,?_)"/]
  v6 --o bind2
  v11 --o bind2
  null --o bind2
  bind2 --as--o v14
  v3 --"a"-->  c23
  bind7[/"count(?taxon)"/]
  v11 --o bind7
  bind7 --as--o v15
  bind8[/"count(?ligandTaxon)"/]
  v12 --o bind8
  bind8 --as--o v16
  bind9[/"count(?cofactorTaxon)"/]
  v13 --o bind9
  bind9 --as--o v17
  bind10[/"count(?catalyticTaxon)"/]
  v14 --o bind10
  bind10 --as--o v18