Takatomo Fujisawa tfuji
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| #!/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
/ refseq2rdf.rb
Created
May 8, 2013 01:41
— forked from ktym/refseq2rdf.rb
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| #!/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 |
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| #!/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
/ ft_rfam.json
Last active
June 30, 2016 09:58
Rfam 12.1 to INSDC feature table mapping based on ftp://ftp.ebi.ac.uk/pub/databases/Rfam/11.0/misc/Rfam2INSDC.types
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| { | |
| "RF00001": { | |
| "AC": "RF00001", | |
| "ID": "5S_rRNA", | |
| "DE": "5S ribosomal RNA", | |
| "feature": "rRNA", | |
| "qualifiers": [ | |
| { | |
| "product": "5S ribosomal RNA" | |
| }, |
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| #!/usr/bin/env ruby | |
| require 'nokogiri' | |
| require 'erb' | |
| #require 'uri' | |
| #require 'pp' | |
| class BioSampleSet | |
| include Enumerable |
tfuji
/ fetch_context.rb
Last active
May 16, 2018 00:23
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| #require 'open-uri' | |
| require 'rdf/raptor' | |
| require 'json' | |
| require 'json/ld' | |
| require 'pp' | |
| require "faraday" | |
| require 'faraday_middleware' | |
| require 'fileutils' | |
| require 'systemu' |
tfuji
/ ncbi_biosample_attributes_extend2ttl.rb
Last active
June 27, 2019 13:41
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| #!/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
/ load_sample.rb
Created
July 1, 2019 06:43
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| #!/usr/bin/env ruby | |
| # | |
| # ruby load_sample.rb biosample/annotated_json dev | |
| require 'elasticsearch' | |
| require 'json' | |
| require 'pp' | |
| #client = Elasticsearch::Client.new({log: true, hosts: { host: 'localhost', user: 'user', password: 'password' }}) | |
| client = Elasticsearch::Client.new({log: true, hosts: { host: 'localhost'}}) |
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| #!/usr/bin/env ruby | |
| require 'elasticsearch' | |
| require 'json' | |
| require 'pp' | |
| begin | |
| #client = Elasticsearch::Client.new({log: true, hosts: { host: 'localhost'}}) | |
| client = Elasticsearch::Client.new({hosts: { host: 'localhost', port: 9291 }}) | |
| q ='water' | |
| from = 0 | |
| size = 20 |
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| { | |
| "@context": [ | |
| "https://schema.org/docs/jsonldcontext.json", | |
| { | |
| "@vocab": "http://togovar.biosciencedbc.jp/ontology/", | |
| "tgv": "http://togovar.biosciencedbc.jp/ontology/", | |
| "dcterms": "http://purl.org/dc/terms/", | |
| "m2r": "http://med2rdf.org/ontology/med2rdf", | |
| "faldo": "http://biohackathon.org/resource/faldo#", | |
| "obo": "http://purl.obolibrary.org/obo/", |
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