The document summarizes activities from LOD Challenge day #02 in Tokyo. It discusses the G-language Project and its G-language Genome Analysis Environment (GAE) web tool. It also describes the G-language Bookmarklet tool, which acts as a gateway for bioinformatics on the web. Further, it outlines Restauro-G version 2, a web service that collects and links related information about genes. It notes capabilities for querying triples from the semantic web, filtering and visualizing linked data, and acknowledging contributions from the G-language Project.

1. LOD Challenge day#02 @ Tokyo
LOD
/ G-language Project
Mail : cory@sfc.keio.ac.jp
Twitter : @adnm

2. 1
G-language Project 1
Web

3. G-language Project
G-language Genome Analysis Environment (G-language GAE)
- Web
-
-

4. Keio Bioinformatics Web Service (KBWS)
Web
Discoverability
Interoperability

5. G-language Bookmarklet
G-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 Data
Web
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

9. Analysis Open Data
& Linked Open Data
Web LOD
Web
LOD

10. Querying interface for Triples
Semantic Web

11. Ring Command for Molecular Biology!

12. Restauro-G version 2
the rapid data broker web-based service that collects and adds
related information about a given gene or gene set

13. Small World & Scale Free
LOD
LOD
LOD

14. Primary Key
=> ID Primary Key LOD
LOD
UniProt ID Primary Key
533049 sequence entries (2011/11/16)
1

15. Gathering Links about “genes”
ID Conversion
Gene 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

16. 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> .

17. Filtering and Visualizing
( ) (Filtering)
(Visualizing)
ex.) http://rest.g-language.org/annotation/FOXP2_HUMAN.n3#Interaction

18. Filtering and Visualizing
LOD
nominal numerical
Cramer's V for nominal data (nominal & nominal)
Spearman’s rank correlation for continuous data
(numerical & numerical)
Fisher’s exact test for enrichment (numerical & nominal)

19. http://ws.g-language.org/toys/bh11/
http://ws.g-language.org/toys/bh11/index2.html

20. Acknowledgement
Kazuharu Arakawa