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UniProt: experimental rhea in use
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JervenBolleman committed Jun 20, 2024
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prefix ex: <https://sparql.uniprot.org/.well-known/sparql-examples/>
prefix up: <http://purl.uniprot.org/core/>
prefix sh: <http://www.w3.org/ns/shacl#>
prefix schema:<https://schema.org/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix faldo:<http://biohackathon.org/resource/faldo#>
prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#>

ex:rhea_reactions_annotated_as_experimental_and_only_small_molecules
a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
sh:prefixes _:sparql_examples_prefixes ;
schema:target <https://sparql.uniprot.org/sparql/> ;
rdfs:comment """Find all rhea (only small molecule) that are used in UniProt where the annotation has a paper and is tagged having experimental evidence."""^^rdf:HTML ;
sh:select """SELECT
?rhea
?catalyzedReaction
?source
WHERE {
{
SELECT
DISTINCT
?rhea
WHERE {
GRAPh<https://sparql.rhea-db.org/rhea> {
?rhea rdfs:subClassOf rh:Reaction .
?rhea rh:side/rh:contains/rh:compound ?compound2 .
?uc rdfs:subClassOf rh:Compound .
}
?compound2 rdfs:subClassOf ?uc .
BIND(IF(?uc = rh:SmallMolecule, 0, 1) AS ?c)
} GROUP BY ?rhea HAVING (SUM(?c) = 0)
}
?catalyzedReaction up:catalyzedReaction ?rhea .
?reif rdf:object ?catalyzedReaction ;
up:attribution ?attr .
?attr up:evidence ECO:0000269 ;
up:source ?source .
?source a up:Citation .
}""" .

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