@prefix ex: <https://www.bgee.org/sparql/.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:001 a sh:SPARQLExecutable,
        sh:SPARQLSelectExecutable ;
    rdfs:comment "What are the ROIs which have the word lymph in its annotation"@en ;
    sh:prefixes _:sparql_examples_prefixes ;
    sh:select """PREFIX ns2: <http://www.openmicroscopy.org/rdf/2016-06/ome_core/>
PREFIX ome:    	<http://www.openmicroscopy.org/rdf/2016-06/ome_core/>                
PREFIX redcap: 	<https://population.ahri.org/api/>
PREFIX rdf:    	<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX dc:     	<http://purl.org/dc/elements/1.1/>
PREFIX dct:		<http://purl.org/dc/terms/>
SELECT DISTINCT ?redCapId ?redcapRecord ?omeID ?omeRecord ?specimen_source ?imagename ?ROI ?text
WHERE {    
  # --- REDCap records ---
  ?redcapRecord
    rdf:type redcap:record ;
    redcap:specimen_source ?specimen_source ;
    redcap:lab_id ?redCapId .
  BIND(
    URI(CONCAT("https://population.ahri.org/api/", REPLACE(STR(?redCapId), " ", "")))
    AS ?redcapConstructedURI
  )
#  VALUES ?specimen_source {"5"}  # restrict to IALCH Forensic Pathology
  # --- OME records ---
  ?omeRecord ome:Map ?map ;
  dct:isPartOf ?image  
  .
  ?map
    ome:Key "lab_id_main" ;
    ome:Value ?omeID . 
  BIND(
    URI(CONCAT("https://population.ahri.org/api/", STR(?omeID)))
    AS ?omeConstructedURI
  )
  .	?image dct:hasPart ?pixels ; ome:Name ?imagename
  .	?pixels rdf:type <http://www.openmicroscopy.org/Schemas/OME/2016-06#Pixels>
	; dct:hasPart ?ROI . 
    ?ROI rdf:type <http://www.openmicroscopy.org/Schemas/OME/2016-06#ROI> ;
    ome:shapes ?shapes .
	?shapes ome:Text ?text
#    VALUES ?text{'lymph node'} .
    FILTER REGEX(?text, 'lymph', 'i')
#  . ?roi dct:isPartOf ?pixels; rdf:type <http://www.openmicroscopy.org/Schemas/OME/2016-06#ROI>

  # --- Match records by constructed URI ---
  FILTER(?redcapConstructedURI = ?omeConstructedURI)
}""" ;
    schema:target <http://localhost:7200/sparql/> .