neXtProt/NXQ_09463

Check there are no entries with a ptm info annotation referring to methylation that do not have the keyword Methylation (KW-0488)

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,"methylat")). # Finds methylated and methylation
  filter not exists {?iso :ptmInfo /:negativeEvidence ?negev} # No negative annotations from neXtProt
  filter not exists {?entry :isoform /:keyword /:term cv:KW-0488.}
  filter (?entry not in (entry:NX_Q93100, entry:NX_P46020, entry:NX_Q9UIF9, entry:NX_Q969L4, entry:NX_Q14683, entry:NX_P46019, entry:NX_P57729)) # Exceptions to rule (not methylated)
}

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((" "))
  c11([":terminology/KW-0488"]):::iri 
  f0[["?entry != ':entry/NX_Q93100'?entry != ':entry/NX_P46020'?entry != ':entry/NX_Q9UIF9'?entry != ':entry/NX_Q969L4'?entry != ':entry/NX_Q14683'?entry != ':entry/NX_P46019'?entry != ':entry/NX_P57729'"]]
  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-0488"]):::iri 
  end
  f1--EXISTS--> f1e0
  f1 --> v1
  f1 --> c8
  f1 --> a1
  f1 --> c9
  f1 --> a2
  f1 --> c10
  f1 --> c11
  v1 --":isoform"-->  a1
  a1 --":keyword"-->  a2
  a2 --":term"-->  c11
  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 --> c12
  f2 --> a3
  f2 --> c13
  f2 --> v3
  v2 --":ptmInfo"-->  a3
  a3 --":negativeEvidence"-->  v3
  f3[["contains(?text,'methylat')"]]
  f3 --> v4
  v1 --":isoform"-->  v2
  v2 --":ptmInfo"-->  a4
  a4 --"rdfs:comment"-->  v4