Satellite meeting for G-language development


Development of REST/SOAP web services for G-language Genome Analysis Environment


  • Kazuharu Arakawa
  • Nobuhiro Kido
  • Kazuki Oshita


 Name: togoWS   -   runs togoWS REST web services

    This is a wrapper around togoWS REST web services provided at
    @ids = togoWS(-search=>"keyword", -db=>"database");

    $entry = togoWS(@ids);

    -search  required option for keyword searching. 
    -db      name of the database for searching and entry retrieval
             required for searching, but not required for entry 
             retrieval, since corresponding database is automatically
             selected from the ID format. However, majority of the 
             databases simply use large numbers as IDs, which all
             result in "pubmed" as the databases. Therefore, use 
             of this option is necessary for IDs that are only numbers.
    -field   field name for entry retrieval (optional)
    -format  format name for entry retrieval (optional)


genome flatfile access

file upload

  • Base URL:
  • Syntax
    • POST a file to fileform=file
    • File types are automatically interpreted by the system. Supported formats are: ABI, ACE, ALF, BSML, CTF, EMBL, Entrez Gene, Exp, FastA, FastQ, GCG, GenBank?, Phd, PIR, PLN, raw, SCF, SWISS.
  • Return
    • Returns a unique reference ID for the uploaded file. You can use this ID for the rest of the analysis so that the large file is not transferred over the network.

genome analysis methods


AJAX/CGI gateway

  • URL:
  • Usage

    • (1)Choose genome file. You can search the species our server has (see following figure) , or load by temporary reference ID or preset genome ID. File upload will be available.
    • (2)Select analysis method from functions list.
    • (3)Results come here and automatically added to History section.
    • (4)All of the analysis you did are available here to check the previous analysis results.
  • TODO
    • [Data load] add file upload form
    • [Analysis] categorize by function orthology
    • [Analysis] hint tip
    • [Analysis] parameter input box
    • [History] 'Send to Galaxy'
    • [History] 'Get analysis result and pass to Galaxy'
    • [History] design improvement
  • Galaxy Connection:
    • access to AJAX/CGI gateway from Galaxy => ok

Perl Wrapper

  • Available at CPAN:
    • simple install with "sudo cpan Bio::Glite"
    • Bio::Glite has all of the functions G-language API, and very efficiently handles data through REST web service of G-language Project. Source code is extremely lightweight (>100KB), and requires very few (mostly standard) modules.