tfuji

#!/usr/bin/env ruby

require 'nokogiri'
#require 'erb'
require 'pp'
require 'json'
#require 'thor'

# 1. wget https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/?format=xml -O ncbi_biosample_attributes.xml
# 2. %ruby ncbi_biosample_attributes_extend2ttl.rb ncbi_biosample_attributes.xml  > biosample_attributes_extend.ttl 

tfuji

#require 'open-uri'
require 'rdf/raptor'
require 'json'
require 'json/ld'
require 'pp'
require "faraday"
require 'faraday_middleware'
require 'fileutils'
require 'systemu'

tfuji

{
  "RF00001": {
    "AC": "RF00001",
    "ID": "5S_rRNA",
    "DE": "5S ribosomal RNA",
    "feature": "rRNA",
    "qualifiers": [
      {
        "product": "5S ribosomal RNA"
      },

tfuji

#!/usr/bin/env ruby

require 'rubygems'
require 'bio'

def parse_st_comment comment
    tagset_id = nil 
    tag_name = tag_value = ''
    st = Hash.new { |h,k| h[k] = {} }
    comment.split("\n").each do |line|

tfuji

#!/usr/bin/env ruby

require 'nokogiri'
require 'erb'
#require 'uri'
#require 'pp'

class BioSampleSet

	include Enumerable

tfuji

#!/usr/bin/env ruby
#
# convert genome_reprots to RDF
# * ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/prokaryotes.txt
# * ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/eukaryotes.txt
#

require 'date'

tfuji

#!/usr/bin/env ruby-1.9

require 'rubygems'
require 'bio'
require 'json'
require 'securerandom'

# [TODO] true to combine the result with the EdgeDB
if $DEBUG
  $edgedb = true