neXtProt/NXQ_09461

Check there are no entries with a ptm info annotation referring to glycosylation that do not have the keyword Glycoprotein (KW-0325)

Use at

• https://sparql.nextprot.org/sparql

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

select distinct ?entry where {  # Include ?text if result is not 0 to identify problem site
  ?entry :isoform ?iso.
  ?iso :ptmInfo /rdfs:comment ?text.
  filter(contains(?text,"glycosylat")). # Finds glycosylated and glycosylation
  filter not exists {?iso :ptmInfo /:negativeEvidence ?negev} # No negative annotations from neXtProt
  filter not exists {?entry :isoform /:keyword /:term cv:KW-0325.}
  filter (?entry not in (entry:NX_O43866, entry:NX_P60827, entry:NX_O75452, entry:NX_P60033, entry:NX_Q01628, entry:NX_O75192, entry:NX_Q8TCT6, entry:NX_Q86TM6, entry:NX_Q8TC12, entry:NX_P49788, entry:NX_Q9NUD9, entry:NX_P47710, entry:NX_Q8IY95, entry:NX_Q02447, entry:NX_P49238, entry:NX_Q9BSG5, entry:NX_Q8TF71, entry:NX_P51811, entry:NX_Q9UBT3, entry:NX_Q9UBY8)) # Exceptions to rule (not glycosylated)
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v1("?entry"):::projected 
  v2("?iso")
  v3("?negev")
  v4("?text")
  a4((" "))
  a3((" "))
  a1((" "))
  a2((" "))
  c24([":terminology/KW-0325"]):::iri 
  f0[["?entry != ':entry/NX_O43866'?entry != ':entry/NX_P60827'?entry != ':entry/NX_O75452'?entry != ':entry/NX_P60033'?entry != ':entry/NX_Q01628'?entry != ':entry/NX_O75192'?entry != ':entry/NX_Q8TCT6'?entry != ':entry/NX_Q86TM6'?entry != ':entry/NX_Q8TC12'?entry != ':entry/NX_P49788'?entry != ':entry/NX_Q9NUD9'?entry != ':entry/NX_P47710'?entry != ':entry/NX_Q8IY95'?entry != ':entry/NX_Q02447'?entry != ':entry/NX_P49238'?entry != ':entry/NX_Q9BSG5'?entry != ':entry/NX_Q8TF71'?entry != ':entry/NX_P51811'?entry != ':entry/NX_Q9UBT3'?entry != ':entry/NX_Q9UBY8'"]]
  f0 --> v1
  f1[["not  "]]
  subgraph f1e0["Exists Clause"]
    e0v1 --":isoform"-->  e0a1
    e0a1 --":keyword"-->  e0a2
    e0a2 --":term"-->  e0c4
    e0v1("?entry"):::projected 
    e0a1((" ")):::projected 
    e0a2((" ")):::projected 
    e0c4([":terminology/KW-0325"]):::iri 
  end
  f1--EXISTS--> f1e0
  f1 --> v1
  f1 --> c21
  f1 --> a1
  f1 --> c22
  f1 --> a2
  f1 --> c23
  f1 --> c24
  v1 --":isoform"-->  a1
  a1 --":keyword"-->  a2
  a2 --":term"-->  c24
  f2[["not  "]]
  subgraph f2e1["Exists Clause"]
    e1v1 --":ptmInfo"-->  e1a1
    e1a1 --":negativeEvidence"-->  e1v2
    e1v1("?iso"):::projected 
    e1v2("?negev"):::projected 
    e1a1((" ")):::projected 
  end
  f2--EXISTS--> f2e1
  f2 --> v2
  f2 --> c25
  f2 --> a3
  f2 --> c26
  f2 --> v3
  v2 --":ptmInfo"-->  a3
  a3 --":negativeEvidence"-->  v3
  f3[["contains(?text,'glycosylat')"]]
  f3 --> v4
  v1 --":isoform"-->  v2
  v2 --":ptmInfo"-->  a4
  a4 --"rdfs:comment"-->  v4