Description of services

• DDBJ
• PDBj
• KEGG
• CBRC

DDBJ

 http://www.xml.nig.ac.jp/index.html

• data retrieve
• sequence search and analysis
• derived DBs
• other DBs

PDBj

KEGG

 http://www.genome.jp/kegg/soap/doc/keggapi_manual.html

first concentrate on sequence + alignment

functional annotations

a given structure with unknown function -> BLAST at DDBJ / KEGG -> no homologs then -> struct-navi

• accession number -> fasta

• PDB ID <-> KEGG GENES ID get_linkdb_between_databases(string:from_db, string:to_db, int:offset, int:limit)

• PDB ID <-> DDDBJ ID

proposed workflow(s)

functional (or structural) annotation of a protein sequence.

Let's call this "funcanot" workflow.

let hits = BLAST_DDBJ(fasta) if func_known(hits) then

return hits

else

let new_hits = BLAST_PDBj(fasta)

if exists(new_hits) then

foreach hit in new_hits do

let shits = struct_navi(hit)

if exists(shits) then

return shits

done

SOAP vs. REST

• SOAP isn't good at huge data (big XML file)?
• REST requires more coding on the client side. User must handle output data (XML or flat text...)
• REST cannot do complicated stuffs?
• No language supports the full SOAP spec.
• Only a few languages have SOAP libraries.

Prototyping funcanot

finally got to real work.... (14:00; 2008-02-12) Prototyping using Taverna.

• Taverna can be used with REST-based WS?