neXtProt/NXQ_09429

Check there are no entries which are PE3-PE4 with an expression-profile annotation with evidence from RNAseq and expression profile detected

Use at

• https://sparql.nextprot.org/sparql

PREFIX : <http://nextprot.org/rdf/>
PREFIX cv: <http://nextprot.org/rdf/terminology/>

select distinct ?entry where {
  ?entry a :Entry.
  ?entry :existence ?pe.
  filter ( ?pe not in (:Evidence_at_protein_level,:Evidence_at_transcript_level,:Uncertain ))
  ?entry :isoform ?iso .
  ?iso :expression /:evidence ?ev.
  ?ev :experimentalContext / :detectionMethod cv:ECO_0000295. # RNA-seq
  ?ev :expressionLevel ?explevel.
  filter (?explevel not in (:Negative,:Low,:Medium,:High))
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v3("?entry"):::projected 
  v5("?ev")
  v1("?explevel")
  v4("?iso")
  v2("?pe")
  a1((" "))
  a2((" "))
  c16([":terminology/ECO_0000295"]):::iri 
  c9([":Entry"]):::iri 
  f0[["?explevel != ':Negative'?explevel != ':Low'?explevel != ':Medium'?explevel != ':High'"]]
  f0 --> v1
  f1[["?pe != ':Evidence_at_protein_level'?pe != ':Evidence_at_transcript_level'?pe != ':Uncertain'"]]
  f1 --> v2
  v3 --"a"-->  c9
  v3 --":existence"-->  v2
  v3 --":isoform"-->  v4
  v4 --":expression"-->  a1
  a1 --":evidence"-->  v5
  v5 --":experimentalContext"-->  a2
  a2 --":detectionMethod"-->  c16
  v5 --":expressionLevel"-->  v1