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.
• 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

• Base URL (list of available analysis methods):
  
  •  http://www.g-language.org/gba/
• Syntax:
  
  • http://www.g-language.org/gb/[genome]/[method]/[required input (if any)]/[option1=value]/[option2=value]...
• Genome data access
  
  • examples:
    
    •  http://www.g-language.org/gba/ecoli/before_startcodon/recA (5' upstream sequence of recA gene)
      
    •  http://www.g-language.org/gba/ecoli/get_geneseq/recA (nucleotide sequence of recA gene)
      
    •  http://www.g-language.org/gba/ecoli/cds (get a list of all feature ids)
• Analysis methods
  
  • examples:
    
    •  http://www.g-language.org/gb/ecoli/gcskew (GC skew analysis - produces a graph)
      
    •  http://www.g-language.org/gb/ecoli/gcskew/cumulative=1 (cumulative GC skew)
      
    •  http://www.g-language.org/gb/ecoli/gcskew/at=1/cumulative=1/output=f/ (cumulative AT skew - output as csv data)
      
    •  http://www.g-language.org/gb/ecoli/gcsi (GC Skew Index analysis - single double value)

SOAP