SIB SPARQL examples

← All examples

144_mature_chain_after_signal_peptide_cleavage

rq turtle/ttl

Find reviewed human secreted proteins where the mature chain begins immediately after the signal peptide is cleaved off

Use at

PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX faldo: <http://biohackathon.org/resource/faldo#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT
  ?protein
  ?signalPeptideEnd
  ?chainName
  ?chainBegin
  ?chainEnd
WHERE {
  ?protein a up:Protein ;
    up:organism taxon:9606 ;
    up:reviewed true ;
    up:annotation ?signalPeptideAnnotation , ?chainAnnotation .
  ?signalPeptideAnnotation a up:Signal_Peptide_Annotation ;
    up:range ?signalPeptideRange .
  ?signalPeptideRange faldo:end/faldo:position ?signalPeptideEnd .
  ?chainAnnotation a up:Chain_Annotation ;
    up:range ?chainRange .
  OPTIONAL { ?chainAnnotation rdfs:comment ?chainName }
  ?chainRange faldo:begin/faldo:position ?chainBegin ;
    faldo:end/faldo:position ?chainEnd .
  FILTER(?chainBegin = ?signalPeptideEnd + 1)
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v5("?chainAnnotation")
  v1("?chainBegin"):::projected 
  v9("?chainEnd"):::projected 
  v8("?chainName"):::projected 
  v7("?chainRange")
  v3("?protein"):::projected 
  v4("?signalPeptideAnnotation")
  v2("?signalPeptideEnd"):::projected 
  v6("?signalPeptideRange")
  a2((" "))
  a3((" "))
  a1((" "))
  c9(["up:Signal_Peptide_Annotation"]):::iri 
  c5(["taxon:9606"]):::iri 
  c13(["up:Chain_Annotation"]):::iri 
  c7(["true^^xsd:boolean"]):::literal 
  c3(["up:Protein"]):::iri 
  f0[["?chainBegin = ?signalPeptideEnd + '1^^xsd:integer'"]]
  f0 --> v1
  f0 --> v2
  v3 --"a"-->  c3
  v3 --"up:organism"-->  c5
  v3 --"up:reviewed"-->  c7
  v3 --"up:annotation"-->  v4
  v3 --"up:annotation"-->  v5
  v4 --"a"-->  c9
  v4 --"up:range"-->  v6
  v6 --"faldo:end"-->  a1
  a1 --"faldo:position"-->  v2
  v5 --"a"-->  c13
  v5 --"up:range"-->  v7
  subgraph optional0["(optional)"]
  style optional0 fill:#bbf,stroke-dasharray: 5 5;
    v5 -."rdfs:comment".->  v8
  end
  v7 --"faldo:begin"-->  a2
  a2 --"faldo:position"-->  v1
  v7 --"faldo:end"-->  a3
  a3 --"faldo:position"-->  v9