|Version 27 (modified by akinjo, 5 years ago)|
Description of services
- data retrieve
- sequence search and analysis
- derived DBs
- other DBs
first concentrate on sequence + alignment
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
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
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.
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?