bio-chembl 0.1.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/.document +5 -0
- data/.project +11 -0
- data/.travis.yml +12 -0
- data/Gemfile +17 -0
- data/Gemfile.lock +33 -0
- data/LICENSE.txt +20 -0
- data/README.md +79 -0
- data/Rakefile +45 -0
- data/VERSION +1 -0
- data/bio-chembl.gemspec +94 -0
- data/lib/bio-chembl.rb +12 -0
- data/lib/bio-chembl/assay.rb +96 -0
- data/lib/bio-chembl/bioactivity.rb +113 -0
- data/lib/bio-chembl/chembl.rb +30 -0
- data/lib/bio-chembl/chemblid.rb +102 -0
- data/lib/bio-chembl/compound.rb +157 -0
- data/lib/bio-chembl/datamodel.rb +25 -0
- data/lib/bio-chembl/rest_api_server.rb +40 -0
- data/lib/bio-chembl/rest_client.rb +264 -0
- data/lib/bio-chembl/target.rb +103 -0
- data/test/helper.rb +18 -0
- data/test/test_bio-chembl-assay.rb +152 -0
- data/test/test_bio-chembl-assay.sh +3 -0
- data/test/test_bio-chembl-chemblid.rb +36 -0
- data/test/test_bio-chembl-chemblid.sh +3 -0
- data/test/test_bio-chembl-compound.rb +125 -0
- data/test/test_bio-chembl-compound.sh +3 -0
- data/test/test_bio-chembl-rest-client.rb +188 -0
- data/test/test_bio-chembl-rest-client.sh +3 -0
- data/test/test_bio-chembl-target.rb +114 -0
- data/test/test_bio-chembl-target.sh +3 -0
- data/test/test_bio-chembl.rb +9 -0
- data/test/test_bio-chembl.sh +3 -0
- metadata +210 -0
data/.document
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data/.project
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data/.travis.yml
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language: ruby
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rvm:
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- 1.9.2
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- 1.9.3
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- jruby-19mode # JRuby in 1.9 mode
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- rbx-19mode
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# - 1.8.7
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# - jruby-18mode # JRuby in 1.8 mode
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# - rbx-18mode
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# uncomment this line if your project needs to run something other than `rake`:
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# script: bundle exec rspec spec
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data/Gemfile
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source "http://rubygems.org"
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# Add dependencies required to use your gem here.
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# Example:
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# gem "activesupport", ">= 2.3.5"
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# Add dependencies to develop your gem here.
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# Include everything needed to run rake, tests, features, etc.
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group :development do
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gem "shoulda", ">= 0"
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gem "rdoc", "~> 3.12"
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gem "bundler", ">= 1.0.0"
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gem "jeweler", "~> 1.8.3"
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gem "bio", ">= 1.4.2"
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gem "rdoc", "~> 3.12"
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gem "curb", ">= 0"
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gem "nokogiri", "~> 1.5.5"
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end
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data/Gemfile.lock
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GEM
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remote: http://rubygems.org/
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specs:
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bio (1.4.2)
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curb (0.8.0)
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git (1.2.5)
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jeweler (1.8.3)
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bundler (~> 1.0)
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git (>= 1.2.5)
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rake
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rdoc
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json (1.7.3)
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nokogiri (1.5.5)
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rake (0.9.2.2)
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rdoc (3.12)
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json (~> 1.4)
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shoulda (3.0.1)
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shoulda-context (~> 1.0.0)
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shoulda-matchers (~> 1.0.0)
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shoulda-context (1.0.0)
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shoulda-matchers (1.0.0)
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PLATFORMS
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ruby
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DEPENDENCIES
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bio (>= 1.4.2)
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bundler (>= 1.0.0)
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curb
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jeweler (~> 1.8.3)
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nokogiri (~> 1.5.5)
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rdoc (~> 3.12)
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shoulda
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data/LICENSE.txt
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Copyright (c) 2012 Mitsuteru Nakao
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.md
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# bio-chembl
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[](http://travis-ci.org/nakao/bioruby-chembl)
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[ChEMBL REST Web Service API](https://www.ebi.ac.uk/chembldb/ws) client, parser and container classes.
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REST API Client
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```ruby
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# Show a web service URI
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BioChEMBL::REST::ChEMBL_URI.compound("CHEMBL1")
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# GET the XML data of the ChEMBL ID CHEMBL1
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api = BioChEMBL::REST.new
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api.compound("CHEMBL1")
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```
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Parser and container
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```ruby
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cpd = BioChEMBL::Compound.find("CHEMBL1")
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cpd.chemblId #=> "CHEMBL1"
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cpd.slimes
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ba = cpd.bioactivities
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assay = BioChEMBL::Assay.find("CHEMBL1217643")
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assay.bioactivities[0].target
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assay.bioactivities[0].parent_compound
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```
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Note: this software is under active development!
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## Installation
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```sh
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gem install bio-chembl
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```
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## Usage
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```ruby
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require 'bio-chembl'
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```
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The API doc is online. For more code examples see the test files in
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the source tree.
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## Project home page
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Information on the source tree, documentation, examples, issues and
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how to contribute, see
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http://github.com/nakao/bio-chembl
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The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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## Todo list
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* BioChEMBL::Target.find_by_refesq method.
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* JSON output support (parser and address).
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* ChEMBL RDF support.
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* Local REST API server with local ChEMBL database.
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## Cite
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If you use this software, please cite one of
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* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
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* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
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## Biogems.info
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This Biogem is published at [#bio-chembl](http://biogems.info/index.html)
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## Copyright
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Copyright (c) 2012 Mitsuteru Nakao. See LICENSE.txt for further details.
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data/Rakefile
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# encoding: utf-8
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require 'rubygems'
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require 'bundler'
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begin
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Bundler.setup(:default, :development)
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rescue Bundler::BundlerError => e
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$stderr.puts e.message
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$stderr.puts "Run `bundle install` to install missing gems"
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exit e.status_code
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end
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require 'rake'
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require 'jeweler'
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Jeweler::Tasks.new do |gem|
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# gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
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gem.name = "bio-chembl"
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gem.homepage = "http://github.com/nakao/bio-chembl"
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gem.license = "MIT"
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gem.summary = %Q{ChEMBL REST API Client, Parser and Container}
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gem.description = %Q{BioRuby plugin for ChEMBL REST API Client, Parser and Container classes}
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gem.email = "mitsuteru.nakao@gmail.com"
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gem.authors = ["Mitsuteru Nakao"]
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# dependencies defined in Gemfile
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end
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Jeweler::RubygemsDotOrgTasks.new
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require 'rake/testtask'
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Rake::TestTask.new(:test) do |test|
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test.libs << 'lib' << 'test'
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test.pattern = 'test/**/test_*.rb'
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test.verbose = true
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end
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task :default => :test
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require 'rdoc/task'
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Rake::RDocTask.new do |rdoc|
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version = File.exist?('VERSION') ? File.read('VERSION') : ""
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rdoc.rdoc_dir = 'rdoc'
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rdoc.title = "bio-chembl #{version}"
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rdoc.rdoc_files.include('README*')
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rdoc.rdoc_files.include('lib/**/*.rb')
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end
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data/VERSION
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0.1.1
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data/bio-chembl.gemspec
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# Generated by jeweler
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# DO NOT EDIT THIS FILE DIRECTLY
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# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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# -*- encoding: utf-8 -*-
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Gem::Specification.new do |s|
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s.name = %q{bio-chembl}
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s.version = "0.1.1"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Mitsuteru Nakao"]
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s.date = %q{2012-07-22}
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s.description = %q{BioRuby plugin for ChEMBL REST API Client, Parser and Container classes}
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s.email = %q{mitsuteru.nakao@gmail.com}
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s.extra_rdoc_files = [
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"LICENSE.txt",
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"README.md"
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]
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s.files = [
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".document",
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".project",
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".travis.yml",
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"Gemfile",
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"Gemfile.lock",
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"LICENSE.txt",
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"README.md",
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"Rakefile",
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"VERSION",
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"bio-chembl.gemspec",
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"lib/bio-chembl.rb",
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"lib/bio-chembl/assay.rb",
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"lib/bio-chembl/bioactivity.rb",
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"lib/bio-chembl/chembl.rb",
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"lib/bio-chembl/chemblid.rb",
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"lib/bio-chembl/compound.rb",
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"lib/bio-chembl/datamodel.rb",
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"lib/bio-chembl/rest_api_server.rb",
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"lib/bio-chembl/rest_client.rb",
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"lib/bio-chembl/target.rb",
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"test/helper.rb",
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"test/test_bio-chembl-assay.rb",
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"test/test_bio-chembl-assay.sh",
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"test/test_bio-chembl-chemblid.rb",
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"test/test_bio-chembl-chemblid.sh",
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"test/test_bio-chembl-compound.rb",
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"test/test_bio-chembl-compound.sh",
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"test/test_bio-chembl-rest-client.rb",
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"test/test_bio-chembl-rest-client.sh",
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"test/test_bio-chembl-target.rb",
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"test/test_bio-chembl-target.sh",
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"test/test_bio-chembl.rb",
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"test/test_bio-chembl.sh"
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]
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s.homepage = %q{http://github.com/nakao/bio-chembl}
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s.licenses = ["MIT"]
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s.require_paths = ["lib"]
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s.rubygems_version = %q{1.3.7}
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s.summary = %q{ChEMBL REST API Client, Parser and Container}
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if s.respond_to? :specification_version then
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current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
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s.specification_version = 3
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if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
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s.add_development_dependency(%q<shoulda>, [">= 0"])
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s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
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s.add_development_dependency(%q<bundler>, [">= 1.0.0"])
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s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
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s.add_development_dependency(%q<bio>, [">= 1.4.2"])
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s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
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s.add_development_dependency(%q<curb>, [">= 0"])
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s.add_development_dependency(%q<nokogiri>, ["~> 1.5.5"])
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else
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s.add_dependency(%q<shoulda>, [">= 0"])
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s.add_dependency(%q<rdoc>, ["~> 3.12"])
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s.add_dependency(%q<bundler>, [">= 1.0.0"])
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s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
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s.add_dependency(%q<bio>, [">= 1.4.2"])
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s.add_dependency(%q<rdoc>, ["~> 3.12"])
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s.add_dependency(%q<curb>, [">= 0"])
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s.add_dependency(%q<nokogiri>, ["~> 1.5.5"])
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end
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else
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s.add_dependency(%q<shoulda>, [">= 0"])
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s.add_dependency(%q<rdoc>, ["~> 3.12"])
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s.add_dependency(%q<bundler>, [">= 1.0.0"])
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s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
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s.add_dependency(%q<bio>, [">= 1.4.2"])
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s.add_dependency(%q<rdoc>, ["~> 3.12"])
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s.add_dependency(%q<curb>, [">= 0"])
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s.add_dependency(%q<nokogiri>, ["~> 1.5.5"])
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end
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end
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data/lib/bio-chembl.rb
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# Please require your code below, respecting the naming conventions in the
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# bioruby directory tree.
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#
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# For example, say you have a plugin named bio-plugin, the only uncommented
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# line in this file would be
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#
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# require 'bio/bio-plugin/plugin'
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#
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# In this file only require other files. Avoid other source code.
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require 'bio-chembl/chembl.rb'
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require 'nokogiri'
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+
require 'bio-chembl/datamodel.rb'
|
3
|
+
require 'bio-chembl/bioactivity.rb'
|
4
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+
|
5
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+
|
6
|
+
module BioChEMBL
|
7
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+
|
8
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+
|
9
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+
|
10
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+
# ChEMBL Assay
|
11
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+
#
|
12
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+
# Data XML
|
13
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+
# <assay>
|
14
|
+
# <chemblId>CHEMBL1217643</chemblId>
|
15
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+
# <assayType>B</assayType>
|
16
|
+
# <journal>Bioorg. Med. Chem. Lett.</journal>
|
17
|
+
# <assayOrganism>Homo sapiens</assayOrganism>
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18
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+
# <assayStrain>Unspecified</assayStrain>
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19
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# <assayDescription>Inhibition of human hERG</assayDescription>
|
20
|
+
# <numBioactivities>1</numBioactivities>
|
21
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+
# </assay>
|
22
|
+
#
|
23
|
+
#
|
24
|
+
class Assay
|
25
|
+
extend BioChEMBL::DataModel
|
26
|
+
|
27
|
+
ATTRIBUTES = [
|
28
|
+
:chemblId,
|
29
|
+
:assayType,
|
30
|
+
:journal,
|
31
|
+
:assayOrganism,
|
32
|
+
:assayStrain,
|
33
|
+
:assayDescription,
|
34
|
+
:numBioactivities
|
35
|
+
]
|
36
|
+
|
37
|
+
set_attr_accessors(ATTRIBUTES)
|
38
|
+
|
39
|
+
|
40
|
+
def self.parse(str)
|
41
|
+
case str
|
42
|
+
when /^</
|
43
|
+
format = 'xml'
|
44
|
+
when /^\{/
|
45
|
+
format = 'json'
|
46
|
+
else
|
47
|
+
raise ArgumentError, "Unexpected file format: #{str.inspect}"
|
48
|
+
end
|
49
|
+
begin
|
50
|
+
eval "self.parse_#{format}(str)"
|
51
|
+
rescue
|
52
|
+
raise NoMethodError
|
53
|
+
end
|
54
|
+
end
|
55
|
+
|
56
|
+
def self.parse_xml(str)
|
57
|
+
xml = Nokogiri::XML(str)
|
58
|
+
this = new
|
59
|
+
eval set_attr_values(ATTRIBUTES)
|
60
|
+
this
|
61
|
+
end
|
62
|
+
|
63
|
+
def self.parse_json(str)
|
64
|
+
raise NotImplementedError
|
65
|
+
end
|
66
|
+
|
67
|
+
def self.parse_rdf(str)
|
68
|
+
raise NotImplementedError
|
69
|
+
end
|
70
|
+
|
71
|
+
def self.find(chemblId)
|
72
|
+
self.parse_xml(REST.new.assays(chemblId))
|
73
|
+
end
|
74
|
+
|
75
|
+
|
76
|
+
# new
|
77
|
+
def initialize(chemblId = nil)
|
78
|
+
@chemblId = chemblId
|
79
|
+
end
|
80
|
+
|
81
|
+
# Resolve the compound data by given ChEMBL ID
|
82
|
+
def resolve
|
83
|
+
resolved = self.class.find(@chemblId)
|
84
|
+
ATTRIBUTES.each do |attr|
|
85
|
+
eval "@#{attr} = resolved.#{attr}"
|
86
|
+
end
|
87
|
+
end
|
88
|
+
|
89
|
+
# ChEMBL Bioactivity
|
90
|
+
def bioactivities
|
91
|
+
BioChEMBL::Bioactivity.parse_list_xml(REST.new.assays(@chemblId, 'bioactivities'))
|
92
|
+
end
|
93
|
+
|
94
|
+
end
|
95
|
+
|
96
|
+
end
|
@@ -0,0 +1,113 @@
|
|
1
|
+
require 'nokogiri'
|
2
|
+
require 'bio-chembl/datamodel.rb'
|
3
|
+
|
4
|
+
|
5
|
+
module BioChEMBL
|
6
|
+
|
7
|
+
# BioChEMBL::Bioactivity
|
8
|
+
#
|
9
|
+
# Data XML
|
10
|
+
# <list>
|
11
|
+
# <bioactivity>
|
12
|
+
# <parent__cmpd__chemblid>CHEMBL1214402</parent__cmpd__chemblid>
|
13
|
+
# <ingredient__cmpd__chemblid>CHEMBL1214402</ingredient__cmpd__chemblid>
|
14
|
+
# <target__chemblid>CHEMBL240</target__chemblid>
|
15
|
+
# <target__confidence>9</target__confidence>
|
16
|
+
# <target__name>HERG</target__name>
|
17
|
+
# <reference>Bioorg. Med. Chem. Lett., (2010) 20:15:4359</reference>
|
18
|
+
# <name__in__reference>26</name__in__reference>
|
19
|
+
# <organism>Homo sapiens</organism>
|
20
|
+
# <bioactivity__type>IC50</bioactivity__type>
|
21
|
+
# <activity__comment>Unspecified</activity__comment>
|
22
|
+
# <operator>=</operator>
|
23
|
+
# <units>nM</units>
|
24
|
+
# <assay__chemblid>CHEMBL1217643</assay__chemblid>
|
25
|
+
# <assay__type>B</assay__type>
|
26
|
+
# <assay__description>Inhibition of human hERG</assay__description>
|
27
|
+
# <value>5900</value>
|
28
|
+
# </bioactivity>
|
29
|
+
# </list>
|
30
|
+
#
|
31
|
+
# Usage
|
32
|
+
#
|
33
|
+
class Bioactivity
|
34
|
+
extend BioChEMBL::DataModel
|
35
|
+
|
36
|
+
ATTRIBUTES = [
|
37
|
+
:parent__cmpd__chemblid,
|
38
|
+
:ingredient__cmpd__chemblid,
|
39
|
+
:target__chemblid,
|
40
|
+
:target__confidence,
|
41
|
+
:target__name,
|
42
|
+
:reference,
|
43
|
+
:name__in__reference,
|
44
|
+
:organism,
|
45
|
+
:bioactivity__type,
|
46
|
+
:activity__comment,
|
47
|
+
:operator,
|
48
|
+
:units,
|
49
|
+
:assay__chemblid,
|
50
|
+
:assay__type,
|
51
|
+
:assay__description,
|
52
|
+
:value
|
53
|
+
]
|
54
|
+
|
55
|
+
set_attr_accessors(ATTRIBUTES)
|
56
|
+
|
57
|
+
def self.parse(str)
|
58
|
+
case str
|
59
|
+
when /^</
|
60
|
+
format = 'xml'
|
61
|
+
when /^\{/
|
62
|
+
format = 'json'
|
63
|
+
else
|
64
|
+
raise ArgumentError, "Unexpected file format: #{str.inspect}"
|
65
|
+
end
|
66
|
+
begin
|
67
|
+
eval "self.parse_#{format}(str)"
|
68
|
+
rescue
|
69
|
+
raise NoMethodError
|
70
|
+
end
|
71
|
+
end
|
72
|
+
|
73
|
+
def self.parse_xml(str)
|
74
|
+
xml = Nokogiri::XML(str)
|
75
|
+
this = new
|
76
|
+
eval set_attr_values(ATTRIBUTES)
|
77
|
+
this
|
78
|
+
end
|
79
|
+
|
80
|
+
# XML
|
81
|
+
# <list><bioactivity> ...
|
82
|
+
def self.parse_list_xml(str)
|
83
|
+
xmls = Nokogiri::XML(str)
|
84
|
+
xmls.xpath("/list/bioactivity").map do |cpd|
|
85
|
+
self.parse_xml(cpd.to_s)
|
86
|
+
end
|
87
|
+
end
|
88
|
+
|
89
|
+
def self.parse_json(str)
|
90
|
+
raise NotImplementedError
|
91
|
+
end
|
92
|
+
|
93
|
+
def self.parse_rdf(str)
|
94
|
+
raise NotImplementedError
|
95
|
+
end
|
96
|
+
|
97
|
+
def parent_compound
|
98
|
+
require 'bio-chembl/compound.rb'
|
99
|
+
BioChEMBL::Compound.find(@parent__cmpd__chemblid)
|
100
|
+
end
|
101
|
+
|
102
|
+
def target
|
103
|
+
require 'bio-chembl/target.rb'
|
104
|
+
BioChEMBL::Target.find(@target__chemblid)
|
105
|
+
end
|
106
|
+
|
107
|
+
def assay
|
108
|
+
require 'bio-chembl/assay.rb'
|
109
|
+
BioChEMBL::Assay.find(@assay__chemblid)
|
110
|
+
end
|
111
|
+
end
|
112
|
+
|
113
|
+
end
|