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Toshiaki Katayama ktym

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  • Database Center for Life Science
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ktym / refseq2rdf.rb
Created September 12, 2012 04:30
Convert RefSeq genome entry into RDF/Turtle using FALDO (BH12)
#!/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
ktym / PfCRT.ttl
Created October 1, 2012 09:19
Example of refseq2rdf_urn.rb (PfCRT gene in NC_004328.2)
@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
ktym / refseq2rdf_urn.rb
Created October 1, 2012 08:58
Convert RefSeq genome entry into RDF/Turtle using FALDO (BH12) and URN
#!/usr/bin/env ruby-1.9
require 'rubygems'
require 'uri'
require 'bio'
require 'json'
require 'securerandom'
# [TODO] integrate this into BioRuby
module Bio
@ktym
ktym / biogitax.rb
Created October 1, 2012 13:54
Classify NCBI GI numbers into given clades (NCBI taxids)
#!/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
ktym / miriam_xml2rdf.rb
Created October 31, 2012 07:51
MIRIAM XML to RDF
#!/usr/bin/env ruby
#
# Convert MIRIAM Registry XML file (http://www.ebi.ac.uk/miriam/main/export/) to RDF
#
# Copyright (C) 2012 Toshiaki Katayama <k@bioruby.org>
#
# 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
ktym / rs_id.json
Last active October 13, 2015 05:27
RefSeq db_xref to Identifiers.org mapping
{
/*
* NCBI RefSeq
*/
"RefSeq": {
"label": "NCBI RefSeq", // custom
"class": "RefSeq",
"prefix": "http://identifiers.org/refseq/"
},
@ktym
ktym / insdc.owl
Created December 12, 2012 08:49
Draft version of INSDC (DDBJ/EMBL/GenBank/RefSeq) ontology in RDF/Turtle format.
@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
ktym / refseq2ttl.rb
Last active December 17, 2015 03:59
refseq2ttl.rb version 8 (migrated into https://github.com/dbcls/rdfsummit/tree/master/insdc2ttl in 2014)
#!/usr/bin/env ruby
require 'rubygems'
require 'uri'
require 'bio'
require 'json'
require 'securerandom'
# [TODO] integrate this into BioRuby
module Bio
@ktym
ktym / .emacs
Last active December 20, 2015 02:09
Configuration for multi-line editing mode in Emacs 24.
;;; library
(let ((default-directory "~/lib/lisp"))
(normal-top-level-add-subdirs-to-load-path))
;; multiple-cursors
; % git clone https://github.com/magnars/multiple-cursors.el.git
; % mv multiple-cursors.el lib/lisp/multiple-cursors
@ktym
ktym / sparql2das.rb
Created January 18, 2014 10:07
Generate BioDAS XML from a SPARQL endpoint which stores genome sequences/annotations using FALDO
#!/usr/bin/env ruby
#
# Usage:
# DAS XML for http://togogenome.org/das/645657/features?segment=NC_017196.1:1,100000 can be generated by
# % ruby sparql2das.rb 645657 features segment=NC_017196.1:1,100000
# With ruby -d option, you'll see debug massages with pretty formatted XML (will miss <?xml> tag though)
#
# TODO:
# Wrap as an Rack app and add X-DAS-* HTTP headers
#