LinkDBのリンク調査
提供:TogoWiki
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 .
- property
- linkdb:equivalent
- URI
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 .
- property
- linkdb:equivalent
- URI; glycoepitope
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 .
- property
- linkdb:equivalent
- URI; glycomedb
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 .
- property
- linkdb:equivalent
- URI; jcggdb
URIについて
- dcterms:identifier無し
- タイプ付けなし
- オントロジーなし
- glycan uri
同じURIがあるか?
LinkDBのGlycoEpitope
- LinkDBのGlycoEpitopeのURI
- GlycoEpitopeのエントリーページ
- http://www.glycoepitope.jp/epitopes/EP0370
- GlycoEpitope RDFのGlycan epitope URIに該当した
- TTL: http://www.glycoepitope.jp/epitopes/glycoepitope.ttl
- http://www.glycoepitope.jp/epitopes/EP0370
LinkDBのGlycomeDB URI
- LinkDBのGlycomeDBのURI
- GlycomeDBのエントリーページ
- GlycomeDB RDFに記述無し
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 .
- LinkDBとGlycomeDBとでは、URIの形が違っていた
- LinkDB
- GlycomeDB
- http://www.genome.jp/dbget-bin/www_bget?gl:G00012
- 詳細ページは同じ表示だが、ドメインがgenome.jp
- http://www.genome.jp/dbget-bin/www_bget?gl:G00012
SPARQLでリンクを作る
GlycomeDB => LinkDB ( KEGG Glycan => LipidBank )
- endpoint; http://test.ts.glytoucan.org/sparql
- graph
- 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 )
- graph
- Glytoucan
- Glytoucan WURCS sequence
- GlycomeDB WURCS sequence
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。
- 329