GlyTouCan RDF data model

Ontology

PrefixNamespaceVocabularies
rdfhttp://www.w3.org/1999/02/22-rdf-syntax-ns#RDF
rdfshttp://www.w3.org/2000/01/rdf-schema#RDF Schema
owlhttp://www.w3.org/2002/07/owl#OWL
xsdhttp://www.w3.org/2001/XMLSchema#XML Schema
foafhttp://xmlns.com/foaf/0.1/FOAF Vocabulary
glycanhttp://purl.jp/bio/12/glyco/glycan#GlycoRDF ontology
glytoucanhttp://www.glytoucan.org/glyco/owl/glytoucan#Glytoucan ontology

Terms of Glytoucan ontology

Classes

Class
glytoucan:derivatized_mass
glytoucan:derivatization_type

Object Properties

PropertyDomainRange
glytoucan:contributorglycan:resource_entryfoaf:person
glytoucan:has_derivatization_typeglycan:derivatized_massglytoucan:derivatization_type
glytoucan:has_derivatized_massglycan:saccharideglytoucan:derivatized_mass

Datatype Properties

PropertyDomainRange
glytoucan:date_registeredxsd:dateTimeStamp
glytoucan:has_massglytoucan:derivatized_massxsd:double
glytoucan:has_primary_idglycan:saccharidexsd:string

Repository RDF semantic relationship

Node and edge

Class
Data (literal, string, integer, double)
Object property
Data property
...
...

URI Construction

Saccharide

Example triple

URI pattern : http://rdf.glycoinfo.org/glycan/{AccessionNumber}

ex：http://rdf.glycoinfo.org/glycan/G00021MO

Derivatized Mass

Example triple

URI pattern : http://rdf.glycoinfo.org/{derivatization type}/{value of the mass}

ex：http://rdf.glycoinfo.org/derivatization_type_none/1176.0175585040001

Derivatization Type

Example triple

None:

http://www.glytoucan.org/glyco/owl/glytoucan#derivatization_type_none

Glycosquence

GlycoCT

Example triple

URI pattern : http://rdf.glycoinfo.org/glycan/{ Accession Number }/glycoct

ex：http://rdf.glycoinfo.org/glycan/G00021MO/glycoct

Component

Example triple

URI pattern : http://rdf.glycoinfo.org/component/{ number of monosaccharide }_{ monosaccharide }

ex：http://rdf.glycoinfo.org/component/1_a-dido-HEX-1%3A5%7C6%3Aa

  • The monosaccharide name is encoded such as "a-dido-HEX-1:5|6:a".

Monosaccharide (Monosaccharide DB RDF web service)

Example triple

URL pattern : http://www.monosaccharidedb.org/rdf/monosaccharide.action?name={monosaccharide name}

ex : http://www.monosaccharidedb.org/rdf/monosaccharide.action?name=a-dido-HEX-1%3A5%7C6%3Aa

Image (glySpace web service)

The structure image previewing with the glySpace web service.

Example triple

URI pattern : http://www.glytoucan.org/glyspace/service/glycans/{ Accession Number }/image?style=extended&format=png&notation={ notation name }

  • CFG

    • http://www..glytoucan.org/glyspace/service/glycans/G00021MO/image?style=extended&format=png&notation=cfg

  • CFG grey scale

    • http://www.glytoucan.org/glyspace/service/glycans/G00021MO/image?style=extended&format=png&notation=cfgbw

  • Oxford

    • http://www.glytoucan.org/glyspace/service/glycans/G00021MO/image?style=extended&format=png&notation=uoxf

  • Oxford color scale

    • http://www.glytoucan.org/glyspace/service/glycans/G00021MO/image?style=extended&format=png&notation=uoxf-color

  • CFG and Oxford

    • http://www.glytoucan.org/glyspace/service/glycans/G00021MO/image?style=extended&format=png&notation=cfg-uoxf

  • IUPAC

    • http://www.glytoucan.org/glyspace/service/glycans/G00021MO/image?style=extended&format=png&notation=iupac

Contributor

Example triple

URI pattern : http://rdf.glycoinfo.org/glytoucan/contributor/userId/{User ID}

ex：http://rdf.glycoinfo.org/glytoucan/contributor/userId/105

Motif (Saccharide)

The motif URI is the same saccharide URI

Example triple

URI pattern : http://rdf.glycoinfo.org/glycan/{AccessionNumber}

ex：http://rdf.glycoinfo.org/glycan/G00021MO

Resource entry (Home page)

Example triple

The resource entry URI is a URL of the Glycan entry at the Glytoucan.

URI pattern : http://www.glytoucan.org/Structures/Glycans/{ Accession Number }

ex：http://www.glytoucan.org/Structures/Glycans/G00021MO

Example RDF Triple

Saccharide

URI pattern

@PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> .

<http://rdf.glycoinfo.org/glycan/G00054MO>
	a	glycan:saccharide .

Glytoucan Accession Number

@PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> .

<http://rdf.glycoinfo.org/glycan/G00054MO>
	a	glycan:saccharide ;
	glytoucan:has_primary_id	"G00054MO" .

Squence

GlycoCT

URI pattern

@PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> .

<http://rdf.glycoinfo.org/glycan/G00054MO>
	a	glycan:saccharide ;
	glycan:has_glycosequence
		<http://rdf.glycoinfo.org/glycan/G00054MO/glycoct> .
		
<http://rdf.glycoinfo.org/glycan/G00054MO/glycoct>
	a	glycan:glycosequence ;
	glycan:in_carbohydrate_format  glycan:carbohydrate_format_glycoct ;
	glycan:has_sequence	
		"RES 1b:b-dglc-HEX-1:5 2s:n-acetyl 3b:a-lgal-HEX-1:5|6:d 4b:b-dgal-HEX-1:5 5b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d 6s:n-acetyl LIN 1:1d(2+1)2n 2:1o(3+1)3d 3:1o(4+1)4d 4:4o(3+2)5d 5:5d(5+1)6n"^^xsd:string .

Mass

Derivatized Mass: URI pattern

Derivatization type: URI pattern

@PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
@PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> .
@PREFIX glytoucan: <http://www.glytoucan.org/glyco/owl/glytoucan#> .

<http://rdf.glycoinfo.org/glycan/G00054MO>
	a	glycan:saccharide ;
	glytoucan:has_derivatized_mass  
		<http://rdf.glycoinfo.org/derivatization_type_none/820.2960859799999> .
		
<http://rdf.glycoinfo.org/derivatization_type_none/820.2960859799999> 
	a	glytoucan:derivatized_mass ;
	glytoucan:has_derivatization_type	glytoucan:derivatization_type_none ;
	glytoucan:has_mass	
		"820.2960859799999"^^xsd:double .

Component

URI pattern

@PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> .

<http://rdf.glycoinfo.org/glycan/G00054MO>
	a	glycan:saccharide ;
	glycan:has_component
		<http://rdf.glycoinfo.org/component/1_b-dglc-HEX-1%3A5%7C%7C%282d%3A1%29n-acetyl> , 
		<http://rdf.glycoinfo.org/component/1_a-lgal-HEX-1%3A5%7C6%3Ad> , 
		<http://rdf.glycoinfo.org/component/1_a-dgro-dgal-NON-2%3A6%7C1%3Aa%7C2%3Aketo%7C3%3Ad%7C%7C%285d%3A1%29n-acetyl> , 
		<http://rdf.glycoinfo.org/component/1_b-dgal-HEX-1%3A5> .
		
<http://rdf.glycoinfo.org/component/1_b-dglc-HEX-1%3A5%7C%7C%282d%3A1%29n-acetyl> 
	a	glycan:component ;
	glycan:has_cardinality     1 ;
	glycan:has_monosaccharide  
		<http://www.monosaccharidedb.org/rdf/monosaccharide.action?name=b-dglc-HEX-1%3A5%7C%7C%282d%3A1%29n-acetyl> .

Monosaccharide

URI pattern

@PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> .

<http://www.monosaccharidedb.org/rdf/monosaccharide.action?name=b-dglc-HEX-1%3A5%7C%7C%282d%3A1%29n-acetyl> 
	a	glycan:monosaccharide .

Image

URI pattern

@PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> .

<http://rdf.glycoinfo.org/glycan/G00054MO>
	a	glycan:saccharide ;
	glycan:has_image  
		<http://www.glytoucan.org/glyspace/service/glycans/G00054MO/image?style=extended&format=png&notation=uoxf-color> ,
		<http://www.glytoucan.org/glyspace/service/glycans/G00054MO/image?style=extended&format=png&notation=iupac> , 
		<http://www.glytoucan.org/glyspace/service/glycans/G00054MO/image?style=extended&format=png&notation=cfgbw> , 
		<http://www.glytoucan.org/glyspace/service/glycans/G00054MO/image?style=extended&format=png&notation=cfg-uoxf> ,
		<http://www.glytoucan.org/glyspace/service/glycans/G00054MO/image?style=extended&format=png&notation=cfg> ,
		<http://www.glytoucan.org/glyspace/service/glycans/G00054MO/image?style=extended&format=png&notation=uoxf> .
		
<http://www.glytoucan.org/glyspace/service/glycans/G00054MO/image?style=extended&format=png&notation=cfg>
	a	glycan:image ;
	glycan:has_symbol_format	glycan:symbol_format_cfg ;
	dc:format	"image/png"^^xsd:string .
  • Notation schema
    • glycan:symbol_format_cfg : CFG
    • glycan:symbol_format_cfg_bw : CFG grey scale
    • glycan:symbol_format_uoxf : Oxford
    • glycan:symbol_format_text : IUPAC
    • glycan:symbol_format_uoxf_color : Oxford color scale
    • glycan:symbol_format_cfg_uoxf : CFG and Oxford

Resource entry ( Home page, Contributor & Contribution Time )

URI pattern

@PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> .
@PREFIX glytoucan: <http://www.glytoucan.org/glyco/owl/glytoucan#> .
@PREFIX xsd:   <http://www.w3.org/2001/XMLSchema#> .

<http://rdf.glycoinfo.org/glycan/G00054MO>
	a	glycan:saccharide ;
	glycan:has_resource_entry
		<http://www.glytoucan.org/Structures/Glycans/G00054MO> .
		
<http://www.glytoucan.org/Structures/Glycans/G00054MO>
        a                          glycan:resource_entry ;
        glycan:in_glycan_database  glytoucan:database_glytoucan ;
        glytoucan:contributor      <http://rdf.glytoucan/contributor/userId/1> ;
        glytoucan:date_registered  "2014-10-20 06:47:31.204"^^xsd:dateTimeStamp .

Contributor

URI pattern

@PREFIX foaf:  <http://xmlns.com/foaf/0.1/> .

<http://rdf.glycoinfo.org/glytoucan/contributor/userId/1>
        a          foaf:Person ;
        foaf:name  "Administrator" .

Motif

URI pattern

@PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> .
@PREFIX foaf:  <http://xmlns.com/foaf/0.1/> .

<http://rdf.glycoinfo.org/glycan/G00054MO>
	a	glycan:saccharide ;
	glycan:has_motif	<http://rdf.glycoinfo.org/glycan/G00054MO> .

<http://rdf.glycoinfo.org/glycan/G00054MO>
	a	glycan:glycan_motif ;
	rdfs:label	"Sialyl Lewis X"@en .
	
// Abbreviated 
<http://rdf.glycoinfo.org/glycan/G00054MO>
	a	glycan:saccharide, glycan:glycan_motif ;
	rdfs:label	"Sialyl Lewis X"@en .
	glycan:has_motif	<http://rdf.glycoinfo.org/glycan/G00054MO> .