# SNV positions within 1000 bp upstream region of MT1A gene in A427 cell line
# Note the SPARQL endpoint for KERO is https://rdfportal.org/rdf/kero/sparql .
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX dcat: <http://www.w3.org/ns/dcat#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX so: <http://purl.obolibrary.org/obo/>
PREFIX dbpedia: <http://dbpedia.org/ontology/>
PREFIX snomed: <http://purl.bioontology.org/ontology/SNOMEDCT/>
PREFIX ensemblvariation: <http://rdf.ebi.ac.uk/terms/ensemblvariation/>
PREFIX faldo: <http://biohackathon.org/resource/faldo#>
PREFIX kero: <http://kero.hgc.jp/ontology/kero.owl#>
SELECT ?snv_position
WHERE
{
?rnadataset a kero:RNAseqDataset ;
kero:hasExpressionData ?rnaseq ;
kero:sample ?sample .
?sample a kero:SampleType ;
rdfs:label "A427" .
?rnaseq a so:SO_0000673 ;
skos:altLabel "MT1A" ;
faldo:location ?rna_region .
?rna_region a faldo:Region ;
faldo:begin ?begin ;
faldo:reference ?chr .
?begin a ?direction ;
faldo:position ?position .
FILTER(?direction = faldo:ForwardStrandPosition OR ?direction = faldo:ReverseStrandPosition)
BIND(IF(?direction = faldo:ForwardStrandPosition, ?position - 1000, ?position) AS ?5position)
BIND(IF(?direction = faldo:ReverseStrandPosition, ?position + 1000, ?position) AS ?3position)
?snv a so:SO_0001483 ;
faldo:location ?snv_location .
?snv_location a faldo:ExactPosition ;
faldo:reference ?chr ;
faldo:position ?snv_position .
?snvdataset a kero:SNVDataset ;
kero:hasVariationSite ?snv ;
kero:sample ?sample .
FILTER(?snv_position > ?5position AND ?snv_position < ?3position)
}