Satellite meeting for G-language development

Topics

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

Participants

• Kazuharu Arakawa
• Nobuhiro Kido
• Kazuki Oshita

REST

genome flatfile access

• Base URL (list of available genomes):
   http://www.g-language.org/gb/
• Syntax:
  
  • http://www.g-language.org/gb/[genome]/[gene]/[feature]
• Genomes (nucleotide composition)
  
  • http://www.g-language.org/gb/[genome]
    • examples:
      
      •  http://www.g-language.org/gb/ecoli (G-language preset genome)
        
      •  http://www.g-language.org/gb/NC_000908 (NCBI RefSeq? accession)
        
      •  http://www.g-language.org/gb/B619CD (G-language REST temporary reference id)
• Genes
  
  • http://www.g-language.org/gb/[genome]/[gene]
    • examples:
      
      •  http://www.g-language.org/gb/ecoli/recA (common gene name)
        
      •  http://www.g-language.org/gb/ecoli/b2699 (canonical gene name / locus tag)
        
      •  http://www.g-language.org/gb/ecoli/FEATURE5804 (G-language feature id)
        
      •  http://www.g-language.org/gb/ecoli/CDS2646 (G-language CDS id)
• features
  
  • http://www.g-language.org/gb/[genome]/[gene]/[feature]
    • examples:
      
      •  http://www.g-language.org/gb/mgen/metX/gene (gene name)
        
      •  http://www.g-language.org/gb/mgen/metX/translation (amino acid sequence)
        
      •  http://www.g-language.org/gb/mgen/*/translation (amino acid sequence of all genes)

file upload

• Base URL:
   http://www.g-language.org/gbi/
• 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.

SOAP