neXtProt/NXQ_09624

Check there are no entries which are PE2-PE4 with a ptm information annotation with positive GOLD experimental evidence from neXtProt and "phosphorylated" in the text

Use at

• https://sparql.nextprot.org/sparql

PREFIX : <http://nextprot.org/rdf/>
PREFIX cv: <http://nextprot.org/rdf/terminology/>
PREFIX source: <http://nextprot.org/rdf/source/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

select distinct ?entry where {
  ?entry a :Entry.
  ?entry :existence ?pe.
  filter ( ?pe not in (:Evidence_at_protein_level,:Uncertain ))
  ?entry :isoform ?iso.
  ?iso :ptmInfo ?ptm.
  ?ptm rdfs:comment ?txt.
  filter (regex (?txt,'phosphorylated'))
  ?ptm :evidence ?ev.
  ?ev :assignedBy source:NextProt.
  ?ev :quality :GOLD.
  filter not exists {?ev :negative 1.}
  ?ev :evidenceCode cv:ECO_0000006. # experimental evidence
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v4("?entry"):::projected 
  v1("?ev")
  v5("?iso")
  v3("?pe")
  v6("?ptm")
  v2("?txt")
  c18([":terminology/ECO_0000006"]):::iri 
  c2(["1^^xsd:integer"]):::literal 
  c7([":Entry"]):::iri 
  c16([":GOLD"]):::iri 
  c14([":source/NextProt"]):::iri 
  f0[["not  "]]
  subgraph f0e0["Exists Clause"]
    e0v1 --":negative"-->  e0c2
    e0v1("?ev"):::projected 
    e0c2(["1^^xsd:integer"]):::literal 
  end
  f0--EXISTS--> f0e0
  f0 --> v1
  f0 --> c1
  f0 --> c2
  v1 --":negative"-->  c2
  f1[["regex(?txt,'phosphorylated')"]]
  f1 --> v2
  f2[["?pe != ':Evidence_at_protein_level'?pe != ':Uncertain'"]]
  f2 --> v3
  v4 --"a"-->  c7
  v4 --":existence"-->  v3
  v4 --":isoform"-->  v5
  v5 --":ptmInfo"-->  v6
  v6 --"rdfs:comment"-->  v2
  v6 --":evidence"-->  v1
  v1 --":assignedBy"-->  c14
  v1 --":quality"-->  c16
  v1 --":evidenceCode"-->  c18