Go to PDBj-DDBj-KEGG/Summary? for the outcome.

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_DAD(fasta) @DDBJ

if func_known(hits) then

send_to_KEGG( hits ) ;; annotation obtained from KEGG

else

let new_hits = BLAST_PDBj(fasta): @DDBJ

if exists(new_hits) then

foreach hit in new_hits do

let shits = struct_navi(hit) :@PDBj

if exists(shits) then

send_to_KEGG( shits );; annotation obtained from KEGG

input	amino acid sequence with unknown function
output	functionally annotated homologs

SOAP vs. REST

• SOAP isn't good at huge data (e.g., big XML file) <-> No problem with REST.
• REST requires more coding on the client side. User must handle output data (XML or flat text...) <-> SOAP can give you the object right away.
• REST cannot do complicated stuffs? (no datatypes, only 4 verbs, etc.)
• 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? -> YES!

Continuing funcanot 2008-02-13

• Taverna cannot really handle conditional branches: workflow just flows but not fork.
• added simple list format option to strnavi REST API.
• Have a Moby lecture?

Continuing funcanot 2008-02-14

• strange behavior:  http://rest.pdbj.org/strnavi?pdbid=2onk&chain=I (when no hits found).

Actually, 2onkI has no structural homologs but for some reason, 2onkI domains 1 and 2 have hits. Why?

• (12:33) One taverna WF done. DDBJ -> PDBj (No KEGG yet) : see attachment.
  • Mostly works, but....
  • Fails with PDB:101m sequence at BLAST_PDB_Parser (  http://rest.pdbj.org/fasta/101m )
• called help as to how to deal with KO SOAP API (Complex Type) -> resolved.
• (14:30) KEGG integrated. So the goal has been achieved!
  • some more debugging required. especially exception handling.
• Debugged.

Sample inputs

•  http://rest.pdbj.org/fasta/1a00/A
•  http://rest.pdbj.org/fasta/101m
•  http://rest.pdbj.org/fasta/1gof
•  http://rest.pdbj.org/fasta/2onk/I
•  http://rest.pdbj.org/fasta/1b54 (hypothetical protein; a good example of structure-based functional (?) annotation)

remarks

Taverna is not so easy to use. required much bean-shell scripting.

• Maybe we should make web services so as to minimize scripting?
• Or prepare a lot of small widgets to handle in/out data formats?

Summarize 2008-02-15

See PDBj-DDBj-KEGG/Summary?