LOD Challenge day#02 @ Tokyo                          LOD                                     / G-language Project        ...
1G-language Project   1Web
G-language ProjectG-language Genome Analysis Environment (G-language GAE)-          Web--
Keio Bioinformatics Web Service (KBWS)Web  Discoverability                    Interoperability
G-language BookmarkletG-language Bookmarklet: a gateway for Bioinformatics on the Web                            K. Arakaw...
Analysis Open DataWeb Web                 LOD
G-language Bookmarklet: Functions.            http://www.g-language.org/wiki/bookmarklet   EMBOSS                         ...
Analysis Open Data           & Linked Open DataWeb           LOD               WebLOD
Querying interface for TriplesSemantic Web
Ring Command for Molecular Biology!
Restauro-G version 2      the rapid data broker web-based service that collects and adds                 related informati...
Small World & Scale FreeLODLOD              LOD
Primary Key=>             ID Primary Key        LOD            LODUniProt                    ID Primary Key  533049 sequen...
Gathering Links about “genes”                 ID ConversionGene                                      IDs cross-referenced ...
Restauro-G version 2                    http://rest.g-language.org/annotation/                     ex.) http://rest.g-lang...
Filtering and Visualizing                    (     )               (Filtering)                                            ...
Filtering and Visualizing               LOD  nominal            numerical  Cramers V for nominal data (nominal & nominal) ...
http://ws.g-language.org/toys/bh11/http://ws.g-language.org/toys/bh11/index2.html
Acknowledgement        Kazuharu Arakawa
LODを用いたバイオインフォマティクスアプリケーション
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LODを用いたバイオインフォマティクスアプリケーション

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第2回LODチャレンジデー in 東京の発表資料です

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LODを用いたバイオインフォマティクスアプリケーション

  1. 1. LOD Challenge day#02 @ Tokyo LOD / G-language Project Mail : cory@sfc.keio.ac.jp Twitter : @adnm
  2. 2. 1G-language Project 1Web
  3. 3. G-language ProjectG-language Genome Analysis Environment (G-language GAE)- Web--
  4. 4. Keio Bioinformatics Web Service (KBWS)Web Discoverability Interoperability
  5. 5. G-language BookmarkletG-language Bookmarklet: a gateway for Bioinformatics on the Web K. Arakawa, N. Kido, K. Oshita, N. Kono, M. Tomita Institute for Advanced Biosciences, Keio University
  6. 6. Analysis Open DataWeb Web LOD
  7. 7. G-language Bookmarklet: Functions. http://www.g-language.org/wiki/bookmarklet EMBOSS Wikipedia G-language Eijiro Google Bio2RDF PubMed EB-eye KEGG/LinkDB Entrez BLAST
  8. 8. Analysis Open Data & Linked Open DataWeb LOD WebLOD
  9. 9. Querying interface for TriplesSemantic Web
  10. 10. Ring Command for Molecular Biology!
  11. 11. Restauro-G version 2 the rapid data broker web-based service that collects and adds related information about a given gene or gene set
  12. 12. Small World & Scale FreeLODLOD LOD
  13. 13. Primary Key=> ID Primary Key LOD LODUniProt ID Primary Key 533049 sequence entries (2011/11/16) 1
  14. 14. Gathering Links about “genes” ID ConversionGene IDs cross-referenced from UniProt KEGG gene - Reaction - Pathway UniProt ID - Brite - KO GO slim ID ID EC number ID Gene ID UniProt ID UniProt
  15. 15. Restauro-G version 2 http://rest.g-language.org/annotation/ ex.) http://rest.g-language.org/annotation/RECA_ECOLI.nt @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>. <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:structure! <http://purl.uniprot.org/pdb/1AA3> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:structure! <http://purl.uniprot.org/pdb/1U98> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:structure! <http://purl.uniprot.org/pdb/1REA> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:sameAs! <http://purl.uniprot.org/embl/U00096> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:structure! <http://purl.uniprot.org/pdb/3CMT> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:structure! <http://purl.uniprot.org/pdb/3CMU> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:seeAlso! <http://purl.uniprot.org/dip/DIP-31832N> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:orthologousOf!<http://purl.uniprot.org/eggnog/COG0468> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:seeAlso! <http://purl.uniprot.org/biocyc/EcoCyc:EG10823-MONOMER> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:seeAlso! <http://purl.uniprot.org/oma/GRDNTIT> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:sameAs! <http://purl.uniprot.org/kegg/eco:b2699> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:structure! <http://purl.uniprot.org/pdb/1XMV> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:sameAs! <http://purl.uniprot.org/refseq/AP_003266.1> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:structure! <http://purl.uniprot.org/pdb/3CMV> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:sameAs! <http://purl.uniprot.org/embl/V00328> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:structure! <http://purl.uniprot.org/pdb/3CMW> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:structure! <http://purl.uniprot.org/eco2dbase/C039.3> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:structure! <http://purl.uniprot.org/pdb/1N03> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:clusterOf! <http://purl.uniprot.org/protclustdb/PRK09354> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:sameAs! <http://purl.uniprot.org/genomereviews/U00096_GR> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:structure! <http://purl.uniprot.org/pdb/2REC> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:sameAs! <http://purl.uniprot.org/genomereviews/AP009048_GR> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:seeAlso! <http://purl.uniprot.org/echobase/EB0816> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:sameAs! <http://purl.uniprot.org/refseq/NP_417179.1> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:sameAs! <http://purl.uniprot.org/ecogene/EG10823> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:structure! <http://purl.uniprot.org/pdb/1XMS> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:sameAs! <http://purl.uniprot.org/geneid/947170> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:seeAlso! <http://purl.uniprot.org/hogenom/HBG339889> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:structure! <http://purl.uniprot.org/pdb/1U99> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:sameAs! <http://purl.uniprot.org/embl/AP009048> . <http://purl.uniprot.org/uniprot/RECA_ECOLI>! rdfs:structure! <http://purl.uniprot.org/pdb/1U94> .
  16. 16. Filtering and Visualizing ( ) (Filtering) (Visualizing) ex.) http://rest.g-language.org/annotation/FOXP2_HUMAN.n3#Interaction
  17. 17. Filtering and Visualizing LOD nominal numerical Cramers V for nominal data (nominal & nominal) Spearman’s rank correlation for continuous data (numerical & numerical) Fisher’s exact test for enrichment (numerical & nominal)
  18. 18. http://ws.g-language.org/toys/bh11/http://ws.g-language.org/toys/bh11/index2.html
  19. 19. Acknowledgement Kazuharu Arakawa

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