@prefix ex: <https://sparql.uniprot.org/.well-known/sparql-examples/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix schema: <https://schema.org/> .
@prefix sh: <http://www.w3.org/ns/shacl#> .

ex:144_mature_chain_after_signal_peptide_cleavage a sh:SPARQLExecutable,
        sh:SPARQLSelectExecutable ;
    rdfs:comment "Find reviewed human secreted proteins where the mature chain begins immediately after the signal peptide is cleaved off"@en ;
    sh:prefixes _:sparql_examples_prefixes ;
    sh:select """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)
}""" ;
    schema:keywords "signal peptide" , "chain" , "molecule processing" ;
    schema:target <https://sparql.uniprot.org/sparql/> .