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

  • 921 views
Uploaded on

第2回LODチャレンジデー in 東京の発表資料です

第2回LODチャレンジデー in 東京の発表資料です

More in: Technology
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Be the first to comment
    Be the first to like this
No Downloads

Views

Total Views
921
On Slideshare
0
From Embeds
0
Number of Embeds
1

Actions

Shares
Downloads
0
Comments
0
Likes
0

Embeds 0

No embeds

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
    No notes for slide

Transcript

  • 1. LOD Challenge day#02 @ Tokyo LOD / G-language Project Mail : cory@sfc.keio.ac.jp Twitter : @adnm
  • 2. 1G-language Project 1Web
  • 3. G-language ProjectG-language Genome Analysis Environment (G-language GAE)- Web--
  • 4. Keio Bioinformatics Web Service (KBWS)Web Discoverability Interoperability
  • 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. Analysis Open DataWeb Web LOD
  • 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. Analysis Open Data & Linked Open DataWeb LOD WebLOD
  • 9. Querying interface for TriplesSemantic Web
  • 10. Ring Command for Molecular Biology!
  • 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. Small World & Scale FreeLODLOD LOD
  • 13. Primary Key=> ID Primary Key LOD LODUniProt ID Primary Key 533049 sequence entries (2011/11/16) 1
  • 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. 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. Filtering and Visualizing ( ) (Filtering) (Visualizing) ex.) http://rest.g-language.org/annotation/FOXP2_HUMAN.n3#Interaction
  • 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. http://ws.g-language.org/toys/bh11/http://ws.g-language.org/toys/bh11/index2.html
  • 19. Acknowledgement Kazuharu Arakawa