# GlycoProtein List (uniprot_glycoprotein.csv)

SELECT DISTINCT ?protein ?protein_name ?p_gene ?prefLabel ?a_gene ?altLabel ?taxon ?scientific_name
WHERE{
  ?protein rdf:type up:Protein .
  ?protein rdfs:label ?protein_name .
  # Gene
  ?protein up:encodedBy ?p_gene .
  ?p_gene skos:prefLabel ?prefLabel .
  OPTIONAL{
    ?protein up:encodedBy ?a_gene .
    ?a_gene skos:altLabel ?altLabel .
  }
  # Organism
  ?protein up:organism ?taxon .
  ?taxon up:scientificName ?scientific_name .
  # Glycosylation
  ?protein up:annotation ?annotation .
  ?annotation a up:Glycosylation_Annotation .
  ?annotation up:range ?range .
  ?range faldo:begin ?begin .
  ?begin faldo:position ?position .
}

# GlycoProtein List (Gene Ontology) (uniprot_glycoprotein_go.csv)

SELECT DISTINCT ?protein ?go ?go_label
WHERE{
  ?protein rdf:type up:Protein .
  ?protein rdfs:label ?protein_name .
  # Gene
  ?protein up:encodedBy ?p_gene .
  ?p_gene skos:prefLabel ?prefLabel .
  OPTIONAL{
    ?protein up:encodedBy ?a_gene .
    ?a_gene skos:altLabel ?altLabel .
  }
  # Organism
  ?protein up:organism ?taxon .
  ?taxon up:scientificName ?scientific_name .
  # Glycosylation
  ?protein up:annotation ?annotation .
  ?annotation a up:Glycosylation_Annotation .
  ?annotation up:range ?range .
  ?range faldo:begin ?begin .
  ?begin faldo:position ?position .
  ?protein up:classifiedWith ?go .
  ?go rdfs:label ?go_label .
}

# GlycoProtein List(Annotation) (uniprot_glycoprotein_annotation.csv)

SELECT DISTINCT ?protein
?annotation_g ?range_g ?begin_g ?position_g
?annotation_t ?range_t ?begin_t ?position_bt ?end_t ?position_et
?annotation_s ?range_s ?begin_s ?position_bs ?end_s ?position_es
WHERE{
  ?protein rdf:type up:Protein .
  ?protein rdfs:label ?protein_name .
  # Gene
  ?protein up:encodedBy ?p_gene .
  ?p_gene skos:prefLabel ?prefLabel .
  OPTIONAL{
    ?protein up:encodedBy ?a_gene .
    ?a_gene skos:altLabel ?altLabel .
  }
  # Organism
  ?protein up:organism ?taxon .
  ?taxon up:scientificName ?scientific_name .

  # Glycosylation
  ?protein up:annotation ?annotation .
  ?annotation a up:Glycosylation_Annotation .
  ?annotation up:range ?range .
  ?range faldo:begin ?begin .
  ?begin faldo:position ?position .
  OPTIONAL{
   ?protein up:annotation ?annotation_t .
   ?annotation_t a up:Transmembrane_Annotation .
   ?annotation_t up:range ?range_t .
   ?range_t faldo:begin ?begin_t .
   ?begin_t faldo:position ?position_bt .
   ?range_t faldo:end ?end_t .
   ?end_t faldo:position ?position_et . }

  OPTIONAL{
   ?protein up:annotation ?annotation_s .
   ?annotation_s a up:Signal_Peptide_Annotation .
   ?annotation_s up:range ?range_s .
   ?range_s faldo:begin ?begin_s .
   ?begin_s faldo:position ?position_bs .
   ?range_s faldo:end ?end_s .
   ?end_s faldo:position ?position_es . }
}