Skip to content

Instantly share code, notes, and snippets.

View ktym's full-sized avatar

Toshiaki Katayama ktym

54 followers · 3 following
  • Database Center for Life Science
  • Japan
View GitHub Profile
@ktym
ktym / taxdump2owl.rb
Last active August 29, 2015 13:56
INSDC (NCBI) taxdump to OWL converter
#!/usr/bin/env ruby
#
# Taxonomy ontology generator
#
# Copyright (C) 2013, 2014 Toshiaki Katayama <ktym@dbcls.jp>
#
# Version: Jan 29, 2014
#
# Usage:
#
@ktym
ktym / d3-sparql-forcegraph.html
Last active August 29, 2015 14:03
<!DOCTYPE html>
<meta charset="utf-8">
<html>
<head>
<!-- Twitter Bootstrap http://getbootstrap.com/2.3.2/ を取得してインストール -->
<link rel="stylesheet" type="text/css" href="lib/bootstrap/css/bootstrap.css"/>
<!-- D3.js http://d3js.org/ を取得してインストール -->
<script src="lib/d3/d3.v3.min.js"></script>
<script>
function query() {
@ktym
ktym / rw-l5.rb
Last active August 29, 2015 14:03
Ruby Warrior Level 5 https://www.bloc.io/ruby-warrior
class Player
def play_turn(warrior)
# cool code goes here
@health ||= warrior.health
if warrior.feel.captive?
warrior.rescue!
elsif warrior.feel.enemy?
warrior.attack!
else
if warrior.health < 20 and !(warrior.health < @health)
@ktym
ktym / jquery-sparql.html
Created July 5, 2014 09:31
<!DOCTYPE html>
<meta charset="utf-8">
<html>
<head>
<!-- Twitter Bootstrap http://getbootstrap.com/2.3.2/ を取得してインストール -->
<link rel="stylesheet" type="text/css" href="bootstrap.css"/>
<!-- jQuery http://jquery.com/ を取得してインストール -->
<script src="jquery.min.js"></script>
<script>
// SPARQL 検索を行う query() 関数を定義
@ktym
ktym / Sample_ruby_native_apps_script.rb
Created October 30, 2014 12:23
Ruby port of the BaseSpace Native App test python script
require 'json'
def metadatajson
json = JSON.parse('
{
"Name": "",
"Description": "",
"HrefAppSession": "",
"Properties": [
{
@ktym
ktym / lodconvert.rb
Last active August 29, 2015 14:09
RDF format converter
#!/usr/bin/env ruby
#
# % gem install linkeddata
# % lodconvert.rb -h
# % lodconvert.rb [-i input_format] [-o output_format] inputfile > outputfile
#
require 'rubygems'
require 'linkeddata'
require 'getoptlong'
@ktym
ktym / ajacs55.md
Last active August 29, 2015 14:26
AJACS 55 Introduction of pathway databases

パスウェイデータベースを使ってみる

Pathguide

まずは、様々なパスウェイデータベースの一覧を見てみましょう。

500 以上のデータベースが下記の分類でリストアップされています。

@ktym
ktym / miriam-xml2csv.rb
Created January 24, 2012 19:39
MIRIAM XML to CSV
#!/usr/bin/env ruby
#
# Convert MIRIAM Registry XML file (http://www.ebi.ac.uk/miriam/main/export/) to CSV
# for browsing at TogoDB (http://semantic.togodb.dbcls.jp/togodb/view/miriam)
#
# Copyright (C) 2012 Toshiaki Katayama <k@bioruby.org>
#
# Pre requirements:
# % curl http://www.ebi.ac.uk/miriam/main/export/xml/ > resources_all.xml
# % gem install nokogiri
@ktym
ktym / taxid2name.rq
Created August 18, 2012 07:48
taxonomy id <-> scientific name
# http://beta.sparql.uniprot.org/
prefix up: <http://purl.uniprot.org/core/>
prefix tax: <http://purl.uniprot.org/taxonomy/>
select *
where {
tax:9606 up:scientificName ?name .
}
@ktym
ktym / ft_so.json
Last active October 10, 2015 06:48
INSDC feature table to OBO sequence ontology mapping based on http://sequenceontology.org/resources/mapping/FT_SO.html
{
"-": {
"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",