@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:166_batch_annotate_gene_list a sh:SPARQLExecutable,
        sh:SPARQLSelectExecutable ;
    rdfs:comment "Given a batch list of UniProt accessions, retrieve one row per entry with its recommended protein name, function description, and reviewed status in a single query. This is the classic 'annotate my differential-expression gene list' BioMart workflow (attributes=c(\\\"name\\\",\\\"description\\\",\\\"reviewed\\\") in one getBM() call)"@en ;
    sh:prefixes _:sparql_examples_prefixes ;
    sh:select """PREFIX up: <http://purl.uniprot.org/core/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/>

SELECT
  ?protein
  ?recommendedName
  (GROUP_CONCAT(?function; separator='\\n') AS ?functions) ?reviewed
WHERE {
  VALUES ?protein { uniprotkb:P04637 uniprotkb:P01308 uniprotkb:Q13613 }
  ?protein up:reviewed ?reviewed .
  OPTIONAL {
    ?protein up:recommendedName ?name .
  }
  OPTIONAL {
    FILTER(!BOUND(?name))
    ?protein up:submittedName ?name .
  }
  ?name up:fullName ?recommendedName .
  OPTIONAL {
    ?protein up:annotation ?functionAnnotation .
    ?functionAnnotation a up:Function_Annotation ;
      rdfs:comment ?function .
  }
} GROUP BY ?protein ?recommendedName ?reviewed""" ;
    schema:keywords "batch lookup" , "gene list" , "annotation" ;
    schema:target <https://sparql.uniprot.org/sparql/> .