ontology-united 0.0.1

checksums.yaml

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data/.rspec

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+--format documentation
+--color

data/.travis.yml

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+language: ruby
+cache: bundler
+rvm:
+  - 2.1.1

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in ontology-united.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2014 Tim Reddehase
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# ontology-united
+
+ontology-united is a small DSL (domain specific language) for
+writing [OWL][owl] ontologies.
+
+It is mainly intended as a gem to be used as part of
+the [ontohub][ontohub] project to create ontologies for testing in
+order to not rely on fixtures. See the corresponding issue
+(ontohub/ontohub#786).
+
+Currently it supports only the [manchester syntax][manchester]
+as serialization
+mechanism and is fairly limited in its owl support.
+However it will be further developed, maintained and extended.
+
+[owl]: http://www.w3.org/TR/owl2-overview/
+[ontohub]: https://github.com/ontohub/ontohub
+[manchester]: http://www.w3.org/2007/OWL/wiki/ManchesterSyntax
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'ontology-united'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install ontology-united
+

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec
+

data/lib/ontology-united/convenience.rb

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+module OntologyUnited
+  module Convenience
+
+    def define_ontology(*args, &block)
+      OntologyUnited::DSL::OntologyDSL.define(*args, &block)
+    end
+
+  end
+end

data/lib/ontology-united/dsl/base_dsl.rb

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+module OntologyUnited
+  module DSL
+    class BaseDSL
+
+      class << self
+
+        attr_writer :stack
+        attr_reader :the_attr_readers
+        attr_reader :current
+
+        def attr_reader_with_default(*readers, default: nil)
+          raise ArgumentError, 'Default value for reader needed' if default.nil?
+          attr_reader *readers
+          @the_attr_readers ||= {}
+          klass = default.is_a?(Class) ? default : default.class
+          readers.each { |reader| @the_attr_readers[reader] = klass }
+        end
+
+        def stack
+          @stack ||= []
+        end
+
+        def current
+          self.stack.last
+        end
+
+      end
+
+      def establish_defaults
+        self.class.the_attr_readers.each do |var, klass|
+          self.instance_variable_set(:"@#{var}", klass.new)
+        end
+      end
+
+      def stack
+        self.class.stack
+      end
+
+      def current
+        self.class.current
+      end
+
+    end
+  end
+end

data/lib/ontology-united/dsl/ontology.rb

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+require 'tempfile'
+require 'set'
+
+module OntologyUnited
+  module DSL
+    class Ontology < BaseDSL
+
+      attr_reader_with_default :the_classes, :the_imports,
+        :the_sentences, :the_prefixes, default: Set
+      attr_reader :name
+
+      def initialize(name)
+        establish_defaults
+        @name = name
+      end
+
+      def elements
+        the_prefixes + the_imports + the_classes + the_sentences
+      end
+
+      def iri
+        create_tempfile if @iri.nil?
+        @iri
+      end
+
+      def class(name=nil)
+        if name.nil?
+          super()
+        else
+          ontology_class = OntologyClass.new(name)
+          the_classes << ontology_class
+          ontology_class
+        end
+      end
+
+      alias_method :ontology_class, :class
+
+      def define(*args, &block)
+        OntologyDSL.define(*args, &block)
+      end
+
+      def imports(arg, &block)
+        if block || arg.is_a?(Ontology)
+          ontology = arg
+          arg = define(ontology.name, &block)
+        end
+        the_import = OntologyImport.new(arg)
+        the_imports << the_import
+        the_import
+      end
+
+      def prefix(prefix, iri=self)
+        the_prefix = OntologyPrefix.new(prefix, iri)
+        the_prefixes << the_prefix
+        the_prefix
+      end
+
+      def sub_class_of(child_ontology_class, parent_ontology_class)
+        sentence = OntologySentence.new([
+          child_ontology_class,
+          'SubClassOf:',
+          parent_ontology_class
+        ])
+        parent_ontology_class.part_of(sentence)
+        the_sentences << sentence
+        sentence
+      end
+
+      def to_s(serializer: OntologyUnited::Serializer::DEFAULT.new)
+        serializer.serialize_ontology(self)
+      end
+
+      def file
+        @file ||= create_tempfile
+      end
+
+      def create_tempfile
+        filename = name.match(%r(([^/]+)\.\w+$))[1]
+        file = Tempfile.new([filename, '.owl'])
+        @iri = "file://#{file.path}"
+        file.write(self.to_s)
+        file.rewind
+        file
+      end
+
+    end
+  end
+end

data/lib/ontology-united/dsl/ontology_class.rb

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+module OntologyUnited
+  module DSL
+    class OntologyClass < OntologyEntityBase
+
+      attr_accessor :prefix
+      attr_reader :name
+      delegate_equality_to method: :name
+
+      def initialize(name)
+        @name = name
+      end
+
+      def sub_class_of(parent_ontology_class)
+        parent.sub_class_of(self, parent_ontology_class)
+      end
+
+      def to_s(serializer: OntologyUnited::Serializer::DEFAULT.new)
+        serializer.serialize_class(self)
+      end
+
+    end
+  end
+end

data/lib/ontology-united/dsl/ontology_dsl.rb

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+module OntologyUnited
+  module DSL
+    class OntologyDSL < BaseDSL
+
+      def self.define(name, &block)
+        ontology = Ontology.new(name)
+        stack.push(ontology)
+        if block
+          if block.arity == 1
+            block.call(ontology)
+          else
+            ontology.instance_eval(&block)
+          end
+        end
+        stack.pop
+        ontology
+      end
+
+    end
+  end
+end

data/lib/ontology-united/dsl/ontology_entity_base.rb

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+module OntologyUnited
+  module DSL
+    class OntologyEntityBase
+
+      attr_reader :the_calls
+
+      def self.delegate_equality_to(method: nil, variable: nil)
+        define_method :eql? do |obj|
+          if method
+            self.send(method.to_sym).eql?(obj.send(method.to_sym))
+          elsif variable
+            own = self.instance_variable_get(:"@#{variable}")
+            other = obj.instance_variable_get(:"@#{variable}")
+            own.eql?(other)
+          end
+        end
+        define_method :hash do
+          if method
+            self.send(method).hash
+          elsif variable
+            self.instance_variable_get(:"@#{variable}")
+          end
+        end
+
+      end
+
+      def parent
+        OntologyDSL.current
+      end
+
+      def part_of(element)
+        @part_of ||= Set.new
+        @part_of << element
+      end
+
+      def part_of?(element)
+        @part_of ||= Set.new
+        @part_of.member?(element)
+      end
+
+      def called_for_parent_before?(method)
+        @the_calls ||= {}
+        !! the_calls[[parent, method]]
+      end
+
+      def eql?(object)
+        (self <=> object) == 0
+      end
+
+    end
+  end
+end

data/lib/ontology-united/dsl/ontology_import.rb

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+module OntologyUnited
+  module DSL
+    class OntologyImport < OntologyEntityBase
+
+      attr_reader :iri, :ontology, :subject
+      delegate_equality_to method: :subject
+
+      def initialize(arg)
+        @iri = arg if arg.is_a?(String)
+        @ontology = arg if arg.is_a?(Ontology)
+        @subject = arg
+      end
+
+      def to_s(serializer: OntologyUnited::Serializer::DEFAULT.new)
+        serializer.serialize_import(self)
+      end
+
+    end
+  end
+end

data/lib/ontology-united/dsl/ontology_prefix.rb

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+module OntologyUnited
+  module DSL
+    class OntologyPrefix < OntologyEntityBase
+
+      attr_reader :prefix, :iri, :ontology, :subject
+      delegate_equality_to method: :prefix
+
+      def initialize(prefix, arg)
+        @prefix = prefix
+        @iri = arg if arg.is_a?(String)
+        @ontology = arg if arg.is_a?(Ontology)
+        @subject = arg
+      end
+
+      def class(name=nil)
+        if name.nil?
+          super()
+        else
+          ontology_class = parent.class(name)
+          ontology_class.prefix = self
+          ontology_class
+        end
+      end
+
+      alias_method :ontology_class, :class
+
+      def apply(ontology_class)
+        "#{prefix}:#{ontology_class.name}"
+      end
+
+      def to_s(serializer: OntologyUnited::Serializer::DEFAULT.new)
+        serializer.serialize_prefix(self)
+      end
+
+    end
+  end
+end

data/lib/ontology-united/dsl/ontology_sentence.rb

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+module OntologyUnited
+  module DSL
+    class OntologySentence < OntologyEntityBase
+
+      attr_reader :sentence
+      delegate_equality_to method: :sentence
+
+      def initialize(sentence)
+        @sentence = sentence
+      end
+
+      def to_s(serializer: OntologyUnited::Serializer::DEFAULT.new)
+        serializer.serialize_sentence(self)
+      end
+
+    end
+  end
+end

data/lib/ontology-united/dsl.rb

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+module OntologyUnited
+  module DSL
+    class Error < ::StandardError; end
+    class NotImplementedError < Error; end
+
+    def self.define_ontology
+
+    end
+  end
+end
+
+require "ontology-united/dsl/base_dsl"
+require "ontology-united/dsl/ontology_entity_base"
+require "ontology-united/dsl/ontology"
+require "ontology-united/dsl/ontology_class"
+require "ontology-united/dsl/ontology_dsl"
+require "ontology-united/dsl/ontology_import"
+require "ontology-united/dsl/ontology_prefix"
+require "ontology-united/dsl/ontology_sentence"

data/lib/ontology-united/serializer/owl/manchester.rb

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+module OntologyUnited::Serializer
+  module OWL
+    class Manchester < SerializerBase
+
+      def serialize_ontology(ontology)
+        process ontology do
+          str = "Ontology: <#{ontology.iri}>\n"
+          str << join(ontology.elements, "\n") do |element|
+            element.to_s(serializer: self)
+          end
+        end
+      end
+
+      def serialize_prefix(ontology_prefix)
+        process ontology_prefix do
+          "Prefix: #{ontology_prefix.prefix}: " <<
+            "<#{ontology_prefix.iri || ontology_prefix.ontology.iri}#>"
+        end
+      end
+
+      def serialize_import(ontology_import)
+        process ontology_import do
+          "Import: <#{ontology_import.iri || ontology_import.ontology.iri}>"
+        end
+      end
+
+      def serialize_class(ontology_class)
+        process ontology_class do
+          prefix = ontology_class.prefix
+          if prefix
+            print_name = prefix.apply(ontology_class)
+          else
+            print_name = "<#{ontology_class.name}>"
+          end
+          "#{'Class: ' if class_definition?(ontology_class)}#{print_name}"
+        end
+      end
+
+      def serialize_sentence(ontology_sentence)
+        opts = {serializer: self}
+        process ontology_sentence do
+          first_class, middle, second_class = ontology_sentence.sentence
+          "#{first_class.to_s(opts)} #{middle} #{second_class.to_s(opts)}"
+        end
+      end
+
+      def class_definition?(ontology_class)
+        # if no parent is set
+        parent_current.nil? ||
+          # or the parent is an ontology itself
+          ontology?(parent_current) ||
+          # or it is the first symbol of a sentence
+          sentence?(parent_current) && parent_current.sentence.first == ontology_class
+      end
+
+    end
+  end
+end

data/lib/ontology-united/serializer/owl.rb

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+module OntologyUnited
+  module Serializer
+    module OWL
+
+    end
+  end
+end
+
+require "ontology-united/serializer/owl/manchester"

data/lib/ontology-united/serializer/serializer_base.rb

@@ -0,0 +1,47 @@
+module OntologyUnited
+  module Serializer
+    class SerializerBase
+      attr_accessor :current, :parent_current
+
+      def initialize(current: nil)
+        self.current = current
+        self.parent_current = nil
+      end
+
+      def process(subject, &block)
+        previous_parent = mark!(subject)
+        result = block.call
+        mark!(parent_current, previous_parent)
+        result
+      end
+
+      def mark!(subject, parent=nil)
+        previous_parent = parent_current
+        parent_current = parent || current
+        current = subject
+        previous_parent
+      end
+
+      def join(elements, sep)
+        elements.reduce('') do |str, raw_element|
+          str << sep unless str.empty?
+          element = yield raw_element
+          str << element
+        end
+      end
+
+      def ontology?(subject)
+        subject.is_a?(OntologyUnited::DSL::Ontology)
+      end
+
+      def class?(subject)
+        subject.is_a?(OntologyUnited::DSL::OntologyClass)
+      end
+
+      def class?(subject)
+        subject.is_a?(OntologyUnited::DSL::OntologySentence)
+      end
+
+    end
+  end
+end

data/lib/ontology-united/serializer.rb

@@ -0,0 +1,8 @@
+require "ontology-united/serializer/serializer_base"
+require "ontology-united/serializer/owl"
+
+module OntologyUnited
+  module Serializer
+    DEFAULT = OWL::Manchester
+  end
+end

data/lib/ontology-united/version.rb

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+module OntologyUnited
+  VERSION = "0.0.1"
+end

data/lib/ontology-united.rb

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+require "ontology-united/version"
+
+module OntologyUnited
+end
+
+require "ontology-united/dsl"
+require "ontology-united/serializer"
+require "ontology-united/convenience"

data/ontology-united.gemspec

@@ -0,0 +1,25 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'ontology-united/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "ontology-united"
+  spec.version       = OntologyUnited::VERSION
+  spec.authors       = ["Tim Reddehase"]
+  spec.email         = ["robustus@rightsrestricted.com"]
+  spec.summary       = %q{small ontology definition dsl}
+  spec.description   = %q{a small domain specific language for writing owl based ontologies}
+  spec.homepage      = "https://github.com/0robustus1/ontology-united"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", ">= 1.5.3"
+  spec.add_development_dependency "rake", "~> 10.2"
+  spec.add_development_dependency "rspec", "~> 2.14"
+  spec.add_development_dependency "pry", "~> 0.9"
+end

data/spec/ontology-united/ontology-united_spec.rb

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+require 'spec_helper'
+require 'uri'
+
+describe OntologyUnited do
+
+  it 'has a version number' do
+    expect(OntologyUnited::VERSION).not_to be nil
+  end
+
+  context 'when issueing a standard definition' do
+    let(:ontology) do
+      OntologyUnited::DSL::OntologyDSL.define('Foo.owl') do
+        rr = prefix('rr', self)
+        imports define('Bar.owl') do
+          rr = prefix('rr', self)
+          rr.class('SomeBar')
+        end
+        rr.class('Bar').sub_class_of rr.class('Foo')
+        rr.class('something')
+        rr.class('something').sub_class_of rr.class('Foo')
+      end
+    end
+
+    it 'should raise no errors' do
+      expect { ontology }.not_to raise_error
+    end
+
+    it 'should have a valid iri' do
+      expect(ontology.iri).to match(URI.regexp)
+    end
+  end
+
+end

data/spec/ontology-united/serializer/owl/manchester_spec.rb

@@ -0,0 +1,60 @@
+require 'spec_helper'
+
+describe OntologyUnited::Serializer::OWL::Manchester do
+  let(:manchester) { OntologyUnited::Serializer::OWL::Manchester }
+  let(:name) { 'OntologyName' }
+  let(:list) do
+    the_prefix, ontology_class, sentence = nil
+    o = OntologyUnited::DSL::OntologyDSL.define("#{name}.owl") do
+      the_prefix = prefix('some', self)
+      ontology_class = the_prefix.class('Foobar')
+      sentence = ontology_class.sub_class_of the_prefix.class('NoBar')
+    end
+    [o, the_prefix, ontology_class, sentence]
+  end
+  let(:ontology) { list[0] }
+  let(:prefix) { list[1] }
+  let(:ontology_class) { list[2] }
+  let(:sentence) { list[3] }
+
+  context 'when serializing an ontology' do
+    let(:serialized) { ontology.to_s(serializer: manchester.new) }
+
+    it 'should contain the prefix definition' do
+      expect(serialized).to include(prefix.to_s(serializer: manchester.new))
+    end
+
+    it 'should contain the ontology class definition' do
+      expect(serialized).to include(ontology_class.to_s(serializer: manchester.new))
+    end
+
+    it 'should contain the sentence definition' do
+      expect(serialized).to include(sentence.to_s(serializer: manchester.new))
+    end
+  end
+
+  context 'when serializing an ontology class' do
+    let(:serialized) { ontology_class.to_s(serializer: manchester.new) }
+
+    it 'should be a valid manchester syntax class definition' do
+      expect(serialized).to eq("Class: some:Foobar")
+    end
+  end
+
+  context 'when serializing a prefix' do
+    let(:serialized) { prefix.to_s(serializer: manchester.new) }
+
+    it 'should be a valid manchester syntax prefix definition' do
+      expect(serialized).to match(/^Prefix: some: <[^>]+#>$/)
+    end
+  end
+
+  context 'when serializing a sentence' do
+    let(:serialized) { sentence.to_s(serializer: manchester.new) }
+
+    it 'should be a valid manchester syntax sentence definition' do
+      expect(serialized).to eq("Class: some:Foobar SubClassOf: Class: some:NoBar")
+    end
+  end
+
+end

data/spec/spec_helper.rb

@@ -0,0 +1,2 @@
+$LOAD_PATH.unshift File.expand_path('../../lib', __FILE__)
+require 'ontology-united'

metadata

@@ -0,0 +1,129 @@
+--- !ruby/object:Gem::Specification
+name: ontology-united
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Tim Reddehase
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-04-24 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.5.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.5.3
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.2'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.2'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.14'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.14'
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.9'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.9'
+description: a small domain specific language for writing owl based ontologies
+email:
+- robustus@rightsrestricted.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".rspec"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/ontology-united.rb
+- lib/ontology-united/convenience.rb
+- lib/ontology-united/dsl.rb
+- lib/ontology-united/dsl/base_dsl.rb
+- lib/ontology-united/dsl/ontology.rb
+- lib/ontology-united/dsl/ontology_class.rb
+- lib/ontology-united/dsl/ontology_dsl.rb
+- lib/ontology-united/dsl/ontology_entity_base.rb
+- lib/ontology-united/dsl/ontology_import.rb
+- lib/ontology-united/dsl/ontology_prefix.rb
+- lib/ontology-united/dsl/ontology_sentence.rb
+- lib/ontology-united/serializer.rb
+- lib/ontology-united/serializer/owl.rb
+- lib/ontology-united/serializer/owl/manchester.rb
+- lib/ontology-united/serializer/serializer_base.rb
+- lib/ontology-united/version.rb
+- ontology-united.gemspec
+- spec/ontology-united/ontology-united_spec.rb
+- spec/ontology-united/serializer/owl/manchester_spec.rb
+- spec/spec_helper.rb
+homepage: https://github.com/0robustus1/ontology-united
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: small ontology definition dsl
+test_files:
+- spec/ontology-united/ontology-united_spec.rb
+- spec/ontology-united/serializer/owl/manchester_spec.rb
+- spec/spec_helper.rb