= 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.

== 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