Ontology

Prefix Namespace
rdf http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs http://www.w3.org/2000/01/rdf-schema#
owl http://www.w3.org/2002/07/owl#
xsd http://www.w3.org/2001/XMLSchema#
foaf http://xmlns.com/foaf/0.1/
bibo http://purl.org/ontology/bibo/
glycan http://purl.jp/bio/12/glyco/glycan#
glytoucan http://www.glytoucan.org/glyco/owl/glytoucan#
wurcs http://www.glycoinfo.org/glyco/owl/wurcs#

GRAPHs

The GlyTouCan RDF consists of multiple Named GRAPHs.

Graph list

Graph Name URI description
Core graph http://rdf.glytoucan.org/core GlyTouCan accession number and a submitted date
WURCS sequence graph http://rdf.glytoucan.org/sequence/wurcs WURCS sequence data
GlycoCT sequence graph http://rdf.glytoucan.org/sequence/glycoct GlycoCT sequence data
Archive graph http://rdf.glytoucan.org/archive Archived glyTouCan accession number

Core graph

URI : http://rdf.glytoucan.org/core

RDF Schema

Triple

@prefix rdf:          <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs:         <http://www.w3.org/2000/01/rdf-schema#> .
@prefix glycan:       <http://purl.jp/bio/12/glyco/glycan#> .
@prefix glytoucan:    <http://www.glytoucan.org/glyco/owl/glytoucan#> .

<http://rdf.glycoinfo.org/glycan/G19529BG>
    rdf:type                   glycan:saccharide;
    glycan:has_resource_entry  <http://rdf.glycoinfo.org/resource-entry/G19529BG>;
    glytoucan:has_primary_id   G19529BG.

<http://rdf.glycoinfo.org/resource-entry/G19529BG>
    rdf:type                   glycan:resource_entry;
    rdfs:seeAlso               <http://glytoucan.org/Structures/Glycans/G19529BG>;
    glytoucan:date_registered  2014-10-31 16:00:57.41;

Archive Graph

Archived entries are included in the archive graph.

URI : http://rdf.glytoucan.org/archive

RDF Schema

Triple

@prefix rdf:          <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs:         <http://www.w3.org/2000/01/rdf-schema#> .
@prefix glycan:       <http://purl.jp/bio/12/glyco/glycan#> .
@prefix glytoucan:    <http://www.glytoucan.org/glyco/owl/glytoucan#> .

<http://rdf.glycoinfo.org/glycan/G68622UR>
    rdf:type      glycan:saccharide;
    rdfs:comment	"Duplication of WURCSs"
    rdfs:seeAlso	<https://glytoucan.org/Structures/Glycans/G88485AW>
    glytoucan:has_primary_id	G68622UR

WURCS graph

URI : http://rdf.glytoucan.org/sequence/wurcs

RDF Schema

RDF (turtle format)

@prefix rdf:	<http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix glycan:	<http://purl.jp/bio/12/glyco/glycan#> .

<http://rdf.glycoinfo.org/glycan/G17266GE>
    glycan:has_glycosequence <http://rdf.glycoinfo.org/glycan/G17266GE/wurcs/2.0> .

<http://rdf.glycoinfo.org/glycan/G17266GE/wurcs/2.0>
    rdf:type	glycan:glycosequence ;
    glycan:has_sequence	"WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-2-3-4-2/a3-b1_a4-c1_a6-g1_c3-d1_c4-e1_e3-f1"^^xsd:string ;
    glycan:in_carbohydrate_format	glycan:carbohydrate_format_wurcs ;

GlycoCT graph

URI : http://rdf.glytoucan.org/sequence/glycoct

RDF Schema

RDF (turtle format)

@prefix rdf:	<http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix glycan:	<http://purl.jp/bio/12/glyco/glycan#> .

<http://rdf.glycoinfo.org/glycan/G35898DT>
  glycan:has_glycosequence  <http://rdf.glycoinfo.org/glycan/G35898DT/glycoct> .

<http://rdf.glycoinfo.org/glycan/G35898DT/glycoct>
		glycan:has_sequence  "RES\n1b:a-dgal-HEX-1:5\n2s:n-acetyl\n3b:b-dgal-HEX-1:5\n4b:b-dglc-HEX-1:5\n5s:n-acetyl\n6b:b-dgal-HEX-1:5\n7b:a-lgal-HEX-1:5|6:d\n8b:b-dglc-HEX-1:5\n9s:n-acetyl\n10b:b-dglc-HEX-1:5\n11s:n-acetyl\n12b:b-dgal-HEX-1:5\n13b:a-lgal-HEX-1:5|6:d\nLIN\n1:1d(2+1)2n\n2:1o(3+1)3d\n3:3o(3+1)4d\n4:4d(2+1)5n\n5:4o(4+1)6d\n6:6o(2+1)7d\n7:3o(6+1)8d\n8:8d(2+1)9n\n9:1o(6+1)10d\n10:10d(2+1)11n\n11:10o(4+1)12d\n12:12o(2+1)13d"^^xsd:string ;
		glycan:carbohydrate_format_glycoct .

Example of SPARQL query for listing valid data in GlyTouCan

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>
PREFIX glytoucan:  <http://www.glytoucan.org/glyco/owl/glytoucan#>

SELECT DISTINCT *
WHERE {
  GRAPH <http://rdf.glytoucan.org/core> {
    ?Saccharide a ?SaClass .
    ?Saccharide glytoucan:has_primary_id ?AccNum .
    ?Saccharide glycan:has_resource_entry ?ResEntry .

    ?ResEntry a ?ResEntryClass .
    ?ResEntry glytoucan:date_registered ?Date .
    ?ResEntry glycan:in_glycan_database ?DB .
    ?ResEntry rdfs:seeAlso ?GlyTouCanURL .
  }
  GRAPH <http://rdf.glytoucan.org/sequence/wurcs> {
    optional {
      ?Saccharide glycan:has_glycosequence ?GSeq .
      ?GSeq a ?GSClass.
      ?GSeq glycan:has_sequence ?WurcsSeq.
      ?GSeq glycan:in_carbohydrate_format ?formatW .
    }
  }
  GRAPH <http://rdf.glytoucan.org/sequence/glycoct> {
    optional {
      ?Saccharide glycan:has_glycosequence ?GSeqCt .
      ?GSeqCt glycan:has_sequence ?CtSeq .
      ?GSeqCt glycan:in_carbohydrate_format ?FormatCT .
    }
  }
  FILTER NOT EXISTS {
   GRAPH <http://rdf.glytoucan.org/archive> {
     ?Saccharide rdf:type ?ArchiveSaccharide
   }
 }
}

=> Run query

Partner Graph

SPARQL query for listing all the GlyTouCan Partner graphs.

SELECT DISTINCT(?g) 
WHERE {
    GRAPH ?g {
        ?s ?p ?o
    }
    FILTER regex(str(?g), "^http://rdf.glytoucan.org/partner/") 
}
ORDER BY ?g

=> Run query