@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:mapping_from_pathology_identifiers_to_external_code_systems_including_ordo a sh:SPARQLExecutable,
        sh:SPARQLSelectExecutable ;
    rdfs:label "Mapping from Pathology Identifiers to external code systems, including ORDO" ;
    rdfs:comment "Mapping from Pathology Identifiers to external code systems, including ORDO"^^rdf:HTML ;
    spex:federatesWith <https://rdfportal.org/bioportal/sparql> ;
    sh:select """PREFIX ome:      <https://ld.openmicroscopy.org/core/>
PREFIX rdfs:     <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos:     <http://www.w3.org/2004/02/skos/core#>
PREFIX ncit:     <http://purl.obolibrary.org/obo/NCIT_>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>

SELECT DISTINCT ?value ?icdo ?ncit ?ncit_label ?umls ?system ?code
WHERE {

  # ── IDR side: collapse to the 70 distinct codes BEFORE federating ──
  {
    SELECT DISTINCT ?value WHERE {
      ?m ome:key "Pathology Identifier" ;
         ome:value ?value .
    }
  }

  BIND(REPLACE(?value, "^M-", "") AS ?raw)
  BIND(IF(STRLEN(?raw) = 5,
          CONCAT(SUBSTR(?raw, 1, 4), "/", SUBSTR(?raw, 5, 1)),
          ?raw) AS ?icdo)

  # ── Federation: one SERVICE round-trip for all 70 codes ──
  SERVICE <https://rdfportal.org/bioportal/sparql> {
    ?ncit ncit:P334 ?icdo ;
          rdfs:label ?ncit_label .
    OPTIONAL { ?ncit ncit:P207 ?umls }

    OPTIONAL {
      ?bridge skos:exactMatch ?ncit ;
              oboInOwl:hasDbXref ?xref .
      BIND(REPLACE(STR(?xref), ":.*",    "") AS ?system)
      BIND(REPLACE(STR(?xref), "^[^:]+:", "") AS ?code)
      FILTER(?system IN
        ("DOID","MONDO","MESH","SCTID","UMLS","Orphanet",
         "OMIM","EFO","HP","MEDGEN","ICDO","MedDRA","GARD"))
    }
  }
}""" ;
    schema:keywords "example" ;
    schema:target <http://idr-sparql.uni-muenster.de/qlever/sparql/> .