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Retrieve drugs that target human enzymes involved in sterol metabolism (federated query with Rhea and ChEMBL via IDSM/Elixir czech republic).

Use at

• https://sparql.uniprot.org/sparql/

PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_>
PREFIX cco: <http://rdf.ebi.ac.uk/terms/chembl#>
PREFIX chebihash: <http://purl.obolibrary.org/obo/chebi#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX up: <http://purl.uniprot.org/core/>

SELECT
        DISTINCT
            ?protein
            ?proteinFullName
            ?activityType
            ?standardActivityValue
            ?standardActivityUnit
            ?chemblMolecule
            ?chemlbMoleculePrefLabel
WHERE
  {
  # ChEBI: retrieve members of the ChEBI class ChEBI:15889 (sterol)
  # Rhea: retrieve the reactions involving these ChEBI as participants
  SERVICE <https://sparql.rhea-db.org/sparql> {
    ?reaction rdfs:subClassOf  rh:Reaction ;
	      rh:status        rh:Approved ;
	      rh:side          ?reactionSide .
    ?reactionSide
	      rh:contains      ?participant .
    ?participant rh:compound  ?compound
    {
      ?compound  rh:chebi  ?chebi .
      ?chebi (rdfs:subClassOf)+ CHEBI:15889
    } UNION {
      ?compound  rh:chebi           ?chebi .
      ?chebi2   rdfs:subClassOf     ?chebiRestriction .
      ?chebiRestriction
		a           owl:Restriction ;
		owl:onProperty      chebihash:has_major_microspecies_at_pH_7_3 ;
		owl:someValuesFrom  ?chebi .
      ?chebi2 (rdfs:subClassOf)+ CHEBI:15889
    }
  }
  # UniProt: retrieve the human (taxid:9606) enzymes catalyzing these Rhea reactions
  ?ca       up:catalyzedReaction  ?reaction .
  ?a        up:catalyticActivity  ?ca .
  ?protein  up:annotation         ?a ;
	    up:organism           taxon:9606 ;
	    up:recommendedName    ?proteinRecName .
  ?proteinRecName
	    up:fullName           ?proteinFullName .
  # Find drugs in wikidata that interact with the UniProt Proteins
  # ChEMBL: retrieve the corresponding targets and with drugs in clinical phase 4
  # Via https://idsm.elixir-czech.cz/sparql/
  SERVICE <https://idsm.elixir-czech.cz/sparql/endpoint/idsm> {
    ?activity a cco:Activity ;
      cco:hasMolecule ?chemblMolecule ;
      cco:hasAssay ?assay ;
      cco:standardType ?activityType ;
      cco:standardValue ?standardActivityValue ;
      cco:standardUnits ?standardActivityUnit .
    ?chemblMolecule cco:highestDevelopmentPhase ?highestDevelopmentPhase ;
      rdfs:label ?chemblMoleculeLabel ;
      skos:prefLabel ?chemlbMoleculePrefLabel .
    FILTER (?highestDevelopmentPhase > 3)
    ?assay cco:hasTarget ?target .
    ?target cco:hasTargetComponent/cco:targetCmptXref ?protein .
    ?protein a cco:UniprotRef .
  }
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v9("?a")
  v14("?activity")
  v17("?activityType"):::projected 
  v16("?assay")
  v8("?ca")
  v5("?chebi")
  v6("?chebi2")
  v7("?chebiRestriction")
  v15("?chemblMolecule"):::projected 
  v20("?chemblMoleculeLabel")
  v21("?chemlbMoleculePrefLabel"):::projected 
  v4("?compound")
  v13("?highestDevelopmentPhase")
  v3("?participant")
  v10("?protein"):::projected 
  v12("?proteinFullName"):::projected 
  v11("?proteinRecName")
  v1("?reaction")
  v2("?reactionSide")
  v19("?standardActivityUnit"):::projected 
  v18("?standardActivityValue"):::projected 
  v22("?target")
  a1((" "))
  c5(["rh:Approved"]):::iri 
  c10(["CHEBI:15889"]):::iri 
  c12(["owl:Restriction"]):::iri 
  c14(["chebihash:has_major_microspecies_at_pH_7_3"]):::iri 
  c3(["rh:Reaction"]):::iri 
  c37(["cco:UniprotRef"]):::iri 
  c20(["taxon:9606"]):::iri 
  c25(["cco:Activity"]):::iri 
  subgraph s1["https://sparql.rhea-db.org/sparql"]
    style s1 stroke-width:4px;
    v1 --"rdfs:subClassOf"-->  c3
    v1 --"rh:status"-->  c5
    v1 --"rh:side"-->  v2
    v2 --"rh:contains"-->  v3
    v3 --"rh:compound"-->  v4
    subgraph union0[" Union "]
    subgraph union0l[" "]
      style union0l fill:#abf,stroke-dasharray: 3 3;
      v4 --"rh:chebi"-->  v5
      v6 --"rdfs:subClassOf"-->  v7
      v7 --"a"-->  c12
      v7 --"owl:onProperty"-->  c14
      v7 --"owl:someValuesFrom"-->  v5
      v6 --"rdfs:subClassOf"-->  c10
    end
    subgraph union0r[" "]
      style union0r fill:#abf,stroke-dasharray: 3 3;
      v4 --"rh:chebi"-->  v5
      v5 --"rdfs:subClassOf"-->  c10
    end
    union0r <== or ==> union0l
    end
  end
  v8 --"up:catalyzedReaction"-->  v1
  v9 --"up:catalyticActivity"-->  v8
  v10 --"up:annotation"-->  v9
  v10 --"up:organism"-->  c20
  v10 --"up:recommendedName"-->  v11
  v11 --"up:fullName"-->  v12
  subgraph s2["https://idsm.elixir-czech.cz/sparql/endpoint/idsm"]
    style s2 stroke-width:4px;
    f0[["?highestDevelopmentPhase > '3^^xsd:integer'"]]
    f0 --> v13
    v14 --"a"-->  c25
    v14 --"cco:hasMolecule"-->  v15
    v14 --"cco:hasAssay"-->  v16
    v14 --"cco:standardType"-->  v17
    v14 --"cco:standardValue"-->  v18
    v14 --"cco:standardUnits"-->  v19
    v15 --"cco:highestDevelopmentPhase"-->  v13
    v15 --"rdfs:label"-->  v20
    v15 --"skos:prefLabel"-->  v21
    v16 --"cco:hasTarget"-->  v22
    v22 --"cco:hasTargetComponent"-->  a1
    a1 --"cco:targetCmptXref"-->  v10
    v10 --"a"-->  c37
  end