ktym

#!/usr/bin/env ruby
#
# Mac OS X webarchive is a binary format of a plist file. You can extract the contents manually:
#  1. convert the plist file into XML by "plutil -convert xml1 file.webarchive"
#  2. parse the resulted XML file by some XML parser
#  3. decode "WebResourceData" by Base64.decode64(data) in each key
#  4. save the decoded content into a file indicated by "WebResourceData"
# Thankfully, the plist library can take care of annoying steps 2 and 3.
#
# Preparation:

ktym

@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix : <http://insdc.org/owl/#> .

<http://insdc.org/owl/>
    a owl:Ontology .

ktym

{
  /*
   * NCBI RefSeq
   */

  "RefSeq": {
    "label": "NCBI RefSeq",  // custom
    "class": "RefSeq",
    "prefix": "http://identifiers.org/refseq/"
  },

ktym

#!/usr/bin/env ruby
#
# Convert MIRIAM Registry XML file (http://www.ebi.ac.uk/miriam/main/export/) to RDF
#
# Copyright (C) 2012 Toshiaki Katayama <[email protected]>
#
# Pre requirements:
#  % curl http://www.ebi.ac.uk/miriam/main/export/xml/ > miriam.xml
#  % gem install nokogiri
#  % miriam_xml2rdf.rb miriam.xml > miriam.rdf

ktym

#!/usr/bin/env ruby-1.9

ENV["BIO_GITAX_DB"] = "#{ENV['HOME']}/ncbi/taxonomy/gitax"

require "rubygems"
require "open-uri"
require "fileutils"

begin
  require "kyotocabinet"

ktym

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .

# SO:chromosome, SO:linear
<urn:uuid:63a091c1-1409-4a91-9f46-db9b04bce8f6>
    <http://genome.db/sw/feature_chromosome> 7 ;
    <http://genome.db/sw/feature_isolate> "3D7" ;
    <http://genome.db/sw/length> 1501717 ;
    <http://genome.db/sw/location> "1..1501717" ;
    <http://genome.db/sw/molecularType> "genomic DNA" ;
    <http://genome.db/sw/organism> "Plasmodium falciparum 3D7" ;

ktym

#!/usr/bin/env ruby-1.9

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

# [TODO] integrate this into BioRuby
module Bio

ktym

#!/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

ktym

{
  "-": {
    "so_id": "SO:0000110",
    "so_term": "located_sequence_feature",
    "ft_desc": "\"-\" is a placeholder for no key; should be used when the need is merely to mark region in order to comment on it or to use it in another feature's location",
    "so_desc": "A biological feature that can be attributed to a region of biological sequence."
  },
  "-10_signal": {
    "so_id": "SO:0000175",
    "so_term": "minus_10_signal",

ktym

#!/usr/bin/env ruby

require "rubygems"
require "net/http"
require "uri"
require "cgi"
require "json"  # gem install json

class SPARQL