Partner Motif Insert

Overview

A GlyTouCan partner has data such as taxonomy, article, external database entry URL. And also it has other data is one of motif data. In update and managemet of motif data as partner data, a entry page of glycan structure be albe to display relation of glycan motif informatin.

What data need for insert?

Partner name
WURCS sequence
WURCSKey
position name (Motif position name)
Motif name

Insert sparql

PREFIX glycan:  <http://purl.jp/bio/12/glyco/glycan#>
PREFIX glytoucan:  <http://www.glytoucan.org/glyco/owl/glytoucan#>
INSERT DATA{
	GRAPH <http://rdf.glytoucan.org/partner/{partner name}>{
		<http://rdf.glycoinfo.org/motif/{position name}/{WURCSKey}> 
			a	glycan:Glycan_motif ;
			glycan:has_glycosequence <http://rdf.glycoinfo.org/motif/{position name}/{WURCSKey}/sequence/wurcs>;
			glytoucan:has_type	glytoucan:Motif_position_{position name}; 
			glycan:has_alias	<http://rdf.glycoinfo.org/motif/{position name}/{WURCSKey}/alias>.

		<http://rdf.glycoinfo.org/motif/{position name}/{WURCSKey}/sequence/wurcs>
			a	glycan:Glycosequence ;
			rdfs:label "{WURCS sequence}"^^xsd:string;
			glycan:has_sequence "{WURCS sequence}"^^xsd:string;
			glycan:in_carbohydrate_format	glycan:carbohydrate_format_wurcs.

		<http://rdf.glycoinfo.org/motif/{position name}/{WURCSKey}/alias>
			a	glytoucan:Glycan_motif_alias ;
			glycan:has_alias_name	"{Motif name}"@en. 
	}
}

Input data

Partner name

This partner name is using in name of partner graph.

bcsdb
glycoepitope
glycome-db
glyconavi

WURCSKey

What is WURCSKey?
- WURCS2md5 + Hash(MD5)
Convert MD5 with WURCS : G00051MO
- WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1
- –> 0401b43b4a36d0b2974e890d77a7b2a4
WURCSKey (ex:G00051MO)
- WURCS2md5=0401b43b4a36d0b2974e890d77a7b2a4

WURCS sequence

ex: “WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1”^^xsd:string

position name

Motif position has 3 type of position name

reducing_end
internal
non_reducing_end

Motif name

“@en” means English language tag

ex: “Lewis X”@en.

Sample RDF of Motif

<http://rdf.glycoinfo.org/motif/non_reducing_end/WURCS2md5=0401b43b4a36d0b2974e890d77a7b2a4> 
	a	glycan:Glycan_motif ;
	glycan:has_glycosequence <http://rdf.glycoinfo.org/motif/non_reducing_end/WURCS2md5=0401b43b4a36d0b2974e890d77a7b2a4/sequence/wurcs>;
	glytoucan:has_type	glytoucan:Motif_type_non_reducing_end;
	glycan:has_alias	<http://rdf.glycoinfo.org/motif/non_reducing_end/WURCS2md5=0401b43b4a36d0b2974e890d77a7b2a4/alias>.

<http://rdf.glycoinfo.org/motif/non_reducing_end/WURCS2md5=0401b43b4a36d0b2974e890d77a7b2a4/sequence/wurcs>
	a	glycan:Glycosequence ;
	rdfs:label "WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1"^^xsd:string;
	glycan:has_sequence "	WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1"^^xsd:string;
	glycan:in_carbohydrate_format	glycan:carbohydrate_format_wurcs.

<http://rdf.glycoinfo.org/motif/non_reducing_end/WURCS2md5=0401b43b4a36d0b2974e890d77a7b2a4/alias>
	a	glytoucan:Glycan_motif_alias ;
	glycan:has_alias_name	"Lewis X"@en.