neXtProt/NXQ_09623

Check there are no entries which are PE2-PE4 with a lipidation site annotation with GOLD experimental evidence which is NOT mass spectrometry from a source other than UniProt

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/>

select distinct ?entry where {
  ?entry a :Entry.
  ?entry :existence ?pe.
  filter ( ?pe not in (:Evidence_at_protein_level,:Uncertain ))
  ?entry :isoform ?iso.
  ?iso :lipidationSite /:evidence ?ev.
  ?ev :assignedBy ?src.
  filter ( ?src not in (source:Uniprot))
  ?ev :quality :GOLD.
  ?ev :evidenceCode ?eco.
  filter (?eco not in (cv:ECO_0001096 )) # mass spectrometry
  ?eco :childOf cv:ECO_0000006. # experimental evidence
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v1("?eco")
  v4("?entry"):::projected 
  v6("?ev")
  v5("?iso")
  v3("?pe")
  v2("?src")
  a1((" "))
  c16([":terminology/ECO_0000006"]):::iri 
  c6([":Entry"]):::iri 
  c13([":GOLD"]):::iri 
  f0[["?eco != ':terminology/ECO_0001096'"]]
  f0 --> v1
  f1[["?src != ':source/Uniprot'"]]
  f1 --> v2
  f2[["?pe != ':Evidence_at_protein_level'?pe != ':Uncertain'"]]
  f2 --> v3
  v4 --"a"-->  c6
  v4 --":existence"-->  v3
  v4 --":isoform"-->  v5
  v5 --":lipidationSite"-->  a1
  a1 --":evidence"-->  v6
  v6 --":assignedBy"-->  v2
  v6 --":quality"-->  c13
  v6 --":evidenceCode"-->  v1
  v1 --":childOf"-->  c16