@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:142_cross_linked_residues a sh:SPARQLExecutable,
        sh:SPARQLSelectExecutable ;
    rdfs:comment "Find reviewed human proteins with a cross-linked residue (e.g. a glycyl lysine isopeptide bond formed by ubiquitin or SUMO conjugation) and the residue position and nature of the cross-link"@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
  ?position
  ?crossLinkType
WHERE {
  ?protein a up:Protein ;
    up:organism taxon:9606 ;
    up:reviewed true ;
    up:annotation ?annotation .
  ?annotation a up:Cross-link_Annotation ;
    rdfs:comment ?crossLinkType ;
    up:range ?range .
  ?range faldo:begin/faldo:position ?position .
}""" ;
    schema:keywords "PTM" , "cross-link" , "ubiquitination" , "post-translational modification" ;
    schema:target <https://sparql.uniprot.org/sparql/> .