48

Retrieve glycosylation sites and glycans on human enzymes (federated with Glyconnect)

Use at

• https://sparql.uniprot.org/sparql/

PREFIX faldo: <http://biohackathon.org/resource/faldo#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX up: <http://purl.uniprot.org/core/>

SELECT
        DISTINCT
            ?protein ?glycosite ?glycostructure ?glycoimage
WHERE{
  ?protein up:annotation ?annotation .
  ?protein up:organism taxon:9606 .
  ?annotation a up:Catalytic_Activity_Annotation .
  ?protein up:sequence ?isoform .
   
  SERVICE <https://glyconnect.expasy.org/sparql> {
    ?glycosite faldo:reference ?isoform .
    ?glycosite faldo:position ?position .
    ?specificglycosite faldo:location ?glycosite .
    ?glycoprotein glycan:glycosylated_at ?specificglycosite .
    ?glycostructure glycan:glycosylates_at ?specificglycosite .
    ?glycostructure foaf:depiction ?glycoimage .
  }
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v2("?annotation")
  v9("?glycoimage"):::projected 
  v7("?glycoprotein")
  v4("?glycosite"):::projected 
  v8("?glycostructure"):::projected 
  v3("?isoform")
  v5("?position")
  v1("?protein"):::projected 
  v6("?specificglycosite")
  c3(["taxon:9606"]):::iri 
  c5(["up:Catalytic_Activity_Annotation"]):::iri 
  v1 --"up:annotation"-->  v2
  v1 --"up:organism"-->  c3
  v2 --"a"-->  c5
  v1 --"up:sequence"-->  v3
  subgraph s1["https://glyconnect.expasy.org/sparql"]
    style s1 stroke-width:4px;
    v4 --"faldo:reference"-->  v3
    v4 --"faldo:position"-->  v5
    v6 --"faldo:location"-->  v4
    v7 --"glycan:glycosylated_at"-->  v6
    v8 --"glycan:glycosylates_at"-->  v6
    v8 --"foaf:depiction"-->  v9
  end