neXtProt/NXQ_00270

Proteins belonging to Rett syndrome pathways, and their subcellular locations (GOLD)

Use at

• https://sparql.nextprot.org/sparql

PREFIX : <http://nextprot.org/rdf/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

select ?entry (str(?gen) AS ?gene) ?pathwayname (group_concat(distinct str(?loclab); SEPARATOR = ",") as ?locs) WHERE {
 SERVICE <https://sparql.wikipathways.org/sparql> {

 {?geneProduct a wp:Protein}
 union
 {?geneProduct a wp:GeneProduct}

 ?geneProduct rdfs:label ?genraw .
 bind (concat( ""^^xsd:string, ?genraw) as ?gen).

 filter(!regex(?gen,"[ a-z-]")). # ensures official gene names for subsequent neXtprot matching
 ?geneProduct dcterms:isPartOf ?pathway .
 ?pathway a wp:Pathway .
 ?pathway wp:organism ?organism .
 filter(contains(str(?organism),"9606"))
 ?pathway dcterms:title ?pathwayname .
 filter(regex(?pathwayname,"rett","i")).
 }
 ?entry a :Entry .
 ?entry :gene / :recommendedName / rdfs:label ?gen .
 ?entry :isoform ?iso.
 ?iso :cellularComponent ?locannot .
 ?locannot :term ?locterm .
 ?locterm rdfs:label ?loclab .
 ?locannot :evidence ?locev .
 ?locev :quality :GOLD .
 filter not exists {?locannot :negativeEvidence ?locev .}
}
group by ?entry ?gen ?pathwayname
order by ?entry

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v1("?entry"):::projected 
  v9("?gen"):::projected 
  v13("?gene")
  v7("?geneProduct")
  v8("?genraw")
  v10("?iso")
  v2("?locannot")
  v3("?locev")
  v12("?loclab"):::projected 
  v14("?locs")
  v11("?locterm")
  v5("?organism")
  v9("?pathway")
  v4("?pathwayname"):::projected 
  a1((" "))
  a2((" "))
  c8(["wp:Protein"]):::iri 
  c12(["wp:Pathway"]):::iri 
  c9(["wp:GeneProduct"]):::iri 
  c15([":Entry"]):::iri 
  c23([":GOLD"]):::iri 
  f0[["not  "]]
  subgraph f0e0["Exists Clause"]
    e0v1 --":negativeEvidence"-->  e0v2
    e0v1("?locannot"):::projected 
    e0v2("?locev"):::projected 
  end
  f0--EXISTS--> f0e0
  f0 --> v2
  f0 --> c1
  f0 --> v3
  v2 --":negativeEvidence"-->  v3
  subgraph s1["https://sparql.wikipathways.org/sparql"]
    style s1 stroke-width:4px;
    f1[["regex(?pathwayname,'rett','i')"]]
    f1 --> v4
    f2[["contains(str(?organism),'9606')"]]
    f2 --> v5
    f3[["not regex(?gen,'#91; a-z-#93;')"]]
    f3 --> v9
    subgraph union0[" Union "]
    subgraph union0l[" "]
      style union0l fill:#abf,stroke-dasharray: 3 3;
      v7 --"a"-->  c9
    end
    subgraph union0r[" "]
      style union0r fill:#abf,stroke-dasharray: 3 3;
      v7 --"a"-->  c8
    end
    union0r <== or ==> union0l
    end
    v7 --"rdfs:label"-->  v8
    bind4[/"concat('',?genraw)"/]
    v8 --o bind4
    bind4 --as--o v9
    v7 --"dcterms:isPartOf"-->  v9
    v9 --"a"-->  c12
    v9 --"wp:organism"-->  v5
    v9 --"dcterms:title"-->  v4
  end
  v1 --"a"-->  c15
  v1 --":gene"-->  a1
  a1 --":recommendedName"-->  a2
  a2 --"rdfs:label"-->  v9
  v1 --":isoform"-->  v10
  v10 --":cellularComponent"-->  v2
  v2 --":term"-->  v11
  v11 --"rdfs:label"-->  v12
  v2 --":evidence"-->  v3
  v3 --":quality"-->  c23
  bind6[/"str(?gen)"/]
  v9 --o bind6
  bind6 --as--o v13
  bind7[/"str(?loclab)"/]
  v12 --o bind7
  bind7 --as--o v14