@prefix ex: <http://idr-sparql.uni-muenster.de/.well-known/sparql-examples/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix schema: <https://schema.org/> .
@prefix sh: <http://www.w3.org/ns/shacl#> .
@prefix spex: <https://purl.expasy.org/sparql-examples/ontology#> .

ex:link_idr_imaging_studies_to_uniprot_proteins_by_pubmed_citation a sh:SPARQLExecutable,
        sh:SPARQLSelectExecutable ;
    rdfs:label "Link IDR imaging studies to UniProt proteins by PubMed citation" ;
    rdfs:comment "A federated query that links IDR imaging studies to UniProt proteins through their shared publication — for every IDR study annotated with a PubMed ID, it lists the UniProt proteins that cite (or are computationally mapped to) that paper."^^rdf:HTML ;
    spex:federatesWith <https://sparql.uniprot.org/sparql> ;
    sh:select """PREFIX ome: <https://ld.openmicroscopy.org/core/>
PREFIX up: <http://purl.uniprot.org/core/>
SELECT ?idrUrl
       (GROUP_CONCAT(DISTINCT STR(?cit);     separator=" ; ") AS ?citations)
       (GROUP_CONCAT(DISTINCT STR(?protein); separator=" ; ") AS ?proteins)
WHERE {
  ?e ome:key "PubMed ID" ; ome:value ?v .
  ?ann ome:mapEntry ?e .
  ?idrSubject ome:hasAnnotation ?ann .
  BIND(CONCAT("https://idr.openmicroscopy.org/webclient/?show=",
              REPLACE(LCASE(STRAFTER(STR(?idrSubject), "openmicroscopy.org/")), "/", "-")) AS ?idrUrl)
  BIND(IRI(CONCAT("http://purl.uniprot.org/citations/", STRBEFORE(?v, " "))) AS ?cit)
  SERVICE <https://sparql.uniprot.org/sparql> {
    ?protein a up:Protein ; (up:citation|up:mappedCitation) ?cit .
  }
}
GROUP BY ?idrUrl""" ;
    schema:keywords "IDR" , "Uniprot" , "DOI" , "PMIDs" , "URL rendered" ;
    schema:target <http://idr-sparql.uni-muenster.de/qlever/sparql/> .