LinkDBのリンク調査

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目次

LinkDBのRDFについて

LinkDB: http://www.genome.jp/linkdb/

KEGG Glycan => 8つのリンクがあった。

  • PubMed
  • CarbBank
  • LipidBank
  • PubChem
  • ChEBI
  • GlycoEpitope
  • GlycomeDB
  • JCGGDB

トリプルについて

Glycan => PubMed

@prefix gl: <http://www.kegg.jp/entry/> .
@prefix linkdb: <http://www.genome.jp/linkdb/> .
@prefix pmid: <http://www.ncbi.nlm.nih.gov/pubmed/> .
gl:G00012	linkdb:original	pmid:12199704	.
gl:G00012	linkdb:original	pmid:7592613	.
  • property
    • linkdb:original

Glycan => CarbBank

@prefix gl: <http://www.kegg.jp/entry/> .
@prefix linkdb: <http://www.genome.jp/linkdb/> .
@prefix pmid: <http://www.ncbi.nlm.nih.gov/pubmed/> .
gl:G00012	linkdb:original	pmid:12199704	.
gl:G00012	linkdb:original	pmid:7592613	.
  • property
    • linkdb:original

Glycan => LipidBank

@prefix gl: <http://www.kegg.jp/entry/> .
@prefix linkdb: <http://www.genome.jp/linkdb/> .
@prefix lipidbank: <http://lipidbank.jp/cgi-bin/detail.cgi?id=> .
gl:G00037	linkdb:equivalent	lipidbank:GSG1202	.
gl:G00039	linkdb:equivalent	lipidbank:GSG1171	.
gl:G00040	linkdb:equivalent	lipidbank:GSG1381	.

Glycan => PubChem

@prefix gl: <http://www.kegg.jp/entry/> .
@prefix linkdb: <http://www.genome.jp/linkdb/> .
@prefix pubchem: <http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=> .
gl:G00001	linkdb:equivalent	pubchem:124490636	.
gl:G00002	linkdb:equivalent	pubchem:124490637	.
gl:G00003	linkdb:equivalent	pubchem:124490638	.
  • property
    • linkdb:equivalent

Glycan => ChEBI

@prefix chebi: <http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:> .
@prefix gl: <http://www.kegg.jp/entry/> .
@prefix linkdb: <http://www.genome.jp/linkdb/> .
gl:G00001	linkdb:equivalent	chebi:18278	.
gl:G00002	linkdb:equivalent	chebi:12427	.
gl:G00003	linkdb:equivalent	chebi:18396	.
  • property
    • linkdb:equivalent

Glycan => GlycoEpitope

@prefix gl: <http://www.kegg.jp/entry/> .
@prefix glycoepitope: <http://www.glyco.is.ritsumei.ac.jp/epitope-bin/epitope.cgi?mode=general&epitope_id=> .
@prefix linkdb: <http://www.genome.jp/linkdb/> .
gl:G00036	linkdb:equivalent	glycoepitope:EP0370	.
gl:G00037	linkdb:equivalent	glycoepitope:EP0114	.
gl:G00037	linkdb:equivalent	glycoepitope:EP0322	.

Glycan => GlycomeDB

@prefix gl: <http://www.kegg.jp/entry/> .
@prefix glycomedb: <http://www.glycome-db.org/database/showStructure.action?glycomeId=> .
@prefix linkdb: <http://www.genome.jp/linkdb/> .
gl:G00001	linkdb:equivalent	glycomedb:1808	.
gl:G00002	linkdb:equivalent	glycomedb:1790	.
gl:G00003	linkdb:equivalent	glycomedb:3688	.

Glycan => JCGGDB

@prefix gl: <http://www.kegg.jp/entry/> .
@prefix jcggdb: <http://jcggdb.jp/idb/jcggdb/> .
@prefix linkdb: <http://www.genome.jp/linkdb/> .
gl:G00001	linkdb:equivalent	jcggdb:JCGG-STR008690	.
gl:G00002	linkdb:equivalent	jcggdb:JCGG-STR008492	.
gl:G00003	linkdb:equivalent	jcggdb:JCGG-STR024580	.

URIについて


同じURIがあるか?

LinkDBのGlycoEpitope

LinkDBのGlycomeDB URI


GlycomeDB RDFで記述されているKEGG glycan entry URI

<http://www.genome.jp/dbget-bin/www_bget?gl:G00012>
      a       owl:NamedIndividual , glycan:resource_entry ;
      glycan:in_glycan_database
              glycan:database_kegg ;
      dcterms:identifier "G00012"^^xsd:string .

SPARQLでリンクを作る

GlycomeDB => LinkDB ( KEGG Glycan => LipidBank )

PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> 
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX linkdb: <http://www.genome.jp/linkdb/> 

SELECT DISTINCT ?gdb ?res_lipidbank 
FROM NAMED <http://rdf.glycoinfo.org/linkdb/glycan_lipidbank>
FROM NAMED <http://rdf.glycoinfo.org/glycome-db>
WHERE{

	# GlycomeDB KEGG Glycan
	GRAPH <http://rdf.glycoinfo.org/glycome-db>{
   		?gdb glycan:has_resource_entry ?res_kegg .
		?res_kegg glycan:in_glycan_database glycan:database_kegg .
		?res_kegg dcterms:identifier ?kegg_id.
   		BIND( iri(replace(str(?res_kegg), "http://www.genome.jp/dbget-bin/www_bget\\?gl:", "http://www.kegg.jp/entry/")) AS ?url)
	}

	GRAPH <http://rdf.glycoinfo.org/linkdb/glycan_lipidbank> {
		?url linkdb:equivalent ?res_lipidbank .
	}

}limit 100



Glytoucan => WURCS sequence => GlycomeDB => LinkDB ( KEGG Glycan => LipidBank )

PREFIX glytoucan: <http://www.glytoucan.org/glyco/owl/glytoucan#>
PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> 
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX linkdb: <http://www.genome.jp/linkdb/> 

SELECT (count(distinct ?AccessionNumber) AS ?countA)
#distinct ?AccessionNumber ?res_lipidbank
FROM NAMED <http://rdf.glytoucan.org>
FROM NAMED <http://rdf.glytoucan.org/sequence/wurcs>
FROM NAMED <http://rdf.glycoinfo.org/glycome-db/sequence/wurcs>
FROM NAMED <http://rdf.glycoinfo.org/glycome-db>
FROM NAMED <http://rdf.glycoinfo.org/linkdb/glycan_lipidbank>
WHERE{
	# Glytoucan
	GRAPH <http://rdf.glytoucan.org>{
		#VALUES ?AccessionNumber { }
		?glytoucan glytoucan:has_primary_id ?AccessionNumber.
	}

	# Glytoucan wurcs sequence
	GRAPH <http://rdf.glytoucan.org/sequence/wurcs>{
		?glytoucan glycan:has_glycosequence ?gseq .
		?gseq glycan:has_sequence ?wurcs .
	}

	# GlycomeDB ID (from wurcs sequence)
	GRAPH <http://rdf.glycoinfo.org/glycome-db/sequence/wurcs>{
		?gdb_gseq glycan:has_sequence ?wurcs .
		?gdb glycan:has_glycosequence ?gdb_gseq .
	}

	# GlycomeDB KEGG Glycan
	GRAPH <http://rdf.glycoinfo.org/glycome-db>{
   		?gdb glycan:has_resource_entry ?res_kegg .
		?res_kegg glycan:in_glycan_database glycan:database_kegg .
		?res_kegg dcterms:identifier ?kegg_id.
   		BIND( iri(replace(str(?res_kegg), "http://www.genome.jp/dbget-bin/www_bget\\?gl:", "http://www.kegg.jp/entry/")) AS ?url)
	}

	GRAPH <http://rdf.glycoinfo.org/linkdb/glycan_lipidbank> {
		?url linkdb:equivalent ?res_lipidbank .
	}

}
  • result
    • 329
      • GlytoucanのAccession number329個に該当するlipidbankのリンクがあった。
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