dbd_onto 0.0.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 15cd696a44197409a3a17797ebf8bcbd93631d9c
+  data.tar.gz: f001d417f57720e846231c268934346025d6fb64
+SHA512:
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data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/.rspec

@@ -0,0 +1,2 @@
+--color
+--format progress

data/.rvmrc

@@ -0,0 +1 @@
+rvm use --create 2.0.0@dbd_onto

data/.travis.yml

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+language: ruby
+bundler_args: --without debug
+script: "bundle exec rspec spec"
+rvm:
+  - 2.0.0
+  - 1.9.3
+  - 1.9.2
+  - jruby-19mode
+  - ruby-head
+  - jruby-head

data/Gemfile

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

data/Guardfile

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+guard :rspec do
+  watch(%r{^spec/.+_spec\.rb$})
+  watch(%r{^lib/(.+)\.rb$})     { |m| "spec/lib/#{m[1]}_spec.rb" }
+  watch('spec/spec_helper.rb')  { "spec" }
+  watch('lib/dbd_onto.rb')      { "spec" }
+end
+

data/HISTORY.txt

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+0.0.1 (2013-06-03)
+=====
+
+* A basic DbdOnto::Provenance ontology
+* bootstrapping with a self referential provenance ontology

data/LICENSE.txt

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+Copyright (c) 2013 Peter Vandenabeele
+
+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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+# DbdOnto
+
+Ontologies for [Dbd].
+
+First a limited Provenance ontology is constructed, because it is required for all facts. This provenance ontology also has a provenance resource (using the provenance predicates defined in itself, to bootstrap the system).
+
+The Provenance ontology uses one meta:defines_predicate attribute from a new Meta ontology. This is needed to describe the definition of predicates, since predicates cannot be the subject of Fact (in Dbd, a subject is an abstract UUID, not a URI, so a link is needed between a resource (all facts with the same subject) and the predicate (that is then the object for this fact that defines the predicate)).
+
+[![Gem Version](https://badge.fury.io/rb/dbd_onto.png)](http://badge.fury.io/rb/dbd_onto)
+[![Build Status](https://travis-ci.org/petervandenabeele/dbd_onto.png?branch=master)](http://travis-ci.org/petervandenabeele/dbd_onto)
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'dbd_onto'
+
+## Usage
+
+Used by Dbd and applications that use Dbd.
+
+## Examples
+
+The ontology is stored as a [Dbd]::Graph. Displaying it in short format:
+
+```
+dbd_onto $ irb
+2.0.0-p195 :001 > require 'dbd_onto'
+ => true
+2.0.0-p195 :002 > DbdOnto::Provenance.new.each {|f| puts f.short} ; nil
+[ prov ] : 44c2dd0f : prov:context             : public
+[ prov ] : 44c2dd0f : prov:source              : https://github.com/petervandenabeele/dbd/blob/d37360070e7f8e6
+[ prov ] : 44c2dd0f : dcterms:creator          : Peter Vandenabeele (@peter_v)
+[ prov ] : 44c2dd0f : dcterms:created          : 2013-05-26 21:30:00 UTC
+[ prov ] : 44c2dd0f : prov:license             : Copyright 2013 Peter Vandenabeele (http://vandenabeele.com), 
+44c2dd0f : e350ae17 : meta:defines_predicate   : prov:context
+44c2dd0f : e350ae17 : rdfs:label               : Context
+44c2dd0f : 5256a1be : meta:defines_predicate   : prov:source
+44c2dd0f : 5256a1be : rdfs:label               : Source
+44c2dd0f : dd57068f : meta:defines_predicate   : prov:license
+44c2dd0f : dd57068f : rdfs:label               : License
+44c2dd0f : 5cddba10 : meta:defines_predicate   : dcterms:creator
+44c2dd0f : 5cddba10 : rdfs:label               : Creator
+44c2dd0f : ece58739 : meta:defines_predicate   : dcterms:created
+44c2dd0f : ece58739 : rdfs:label               : Created
+ => nil
+2.0.0-p195 :003 > DbdOnto::Meta.new.each {|f| puts f.short} ; nil
+[ prov ] : b75f3b8c : prov:context             : public
+[ prov ] : b75f3b8c : prov:source              : https://github.com/petervandenabeele/dbd_onto/blob/08adb5bf0e
+[ prov ] : b75f3b8c : dcterms:creator          : Peter Vandenabeele (@peter_v)
+[ prov ] : b75f3b8c : dcterms:created          : 2013-06-03 21:00:00 UTC
+[ prov ] : b75f3b8c : prov:license             : Copyright 2013 Peter Vandenabeele (http://vandenabeele.com), 
+b75f3b8c : bd07e072 : meta:defines_predicate   : meta:defines_predicate
+b75f3b8c : bd07e072 : rdfs:label               : Defines predicate
+ => nil 
+```
+
+[Dbd]:              https://github.com/petervandenabeele/dbd#readme

data/Rakefile

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+require "bundler/gem_tasks"

data/dbd_onto.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'dbd_onto/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "dbd_onto"
+  spec.version       = DbdOnto::VERSION
+  spec.authors       = ["Peter Vandenabeele"]
+  spec.email         = ["peter@vandenabeele.com"]
+  spec.description   = %q{Ontologies for Dbd}
+  spec.summary       = %q{Ontologies for Dbd}
+  spec.homepage      = ""
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency 'bundler', '>= 1.2.4'
+  spec.add_development_dependency 'rake'
+  spec.add_development_dependency 'guard-rspec'
+  spec.add_development_dependency 'terminal-notifier-guard'
+  spec.add_development_dependency 'yard'
+  spec.add_runtime_dependency 'rdf', '~> 1.0.6'
+  spec.add_runtime_dependency 'ruby_peter_v', '>= 0.0.8'
+  spec.add_runtime_dependency 'dbd', '>= 0.0.5'
+end

data/lib/dbd_onto/base.rb

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+module DbdOnto
+  class Base < Dbd::Graph
+    include ProvenanceMethods
+    include FactMethods
+  end
+end

data/lib/dbd_onto/fact_methods.rb

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+module DbdOnto
+  module FactMethods
+
+    def fact_label(attribute)
+      # TODO in Dbd : turn predicate into a proper Predicate class
+      Dbd::Fact.new(predicate: RDF::RDFS.label.qname.join(':'), object: attribute.gsub(/_/,' ').capitalize)
+    end
+
+  end
+end

data/lib/dbd_onto/meta.rb

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+module DbdOnto
+  class Meta < Base
+
+    META_ATTRIBUTES = %w(defines_predicate)
+
+    def initialize
+      super
+      self << provenance
+      self << meta_resources
+    end
+
+  private
+
+    def provenance_attributes
+      [
+       #[predicate, object]
+        ['prov:context', 'public'],
+        ['prov:source' , 'https://github.com/petervandenabeele/dbd_onto/blob/08adb5bf0ed5cd259ad4d31d9d8ebbbe230c66b1/lib/dbd_onto/provenance.rb'],
+        ['dcterms:creator' , 'Peter Vandenabeele (@peter_v)'],
+        ['dcterms:created', Time.new(2013,6,3,23,0,0,'+02:00').utc],
+        ['prov:license', 'Copyright 2013 Peter Vandenabeele (http://vandenabeele.com), licensed under MIT license.']
+      ]
+    end
+
+    def meta_resources
+      META_ATTRIBUTES.map do |attribute|
+        resource = Dbd::Resource.new(provenance_subject: provenance.subject)
+        resource << fact_defines_predicate_meta(attribute)
+        resource << fact_label(attribute)
+      end
+    end
+
+    def fact_defines_predicate_meta(attribute)
+      Dbd::Fact.new(predicate: 'meta:defines_predicate', object: "meta:#{attribute}")
+    end
+
+  end
+end

data/lib/dbd_onto/provenance.rb

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+module DbdOnto
+  class Provenance < Base
+
+    PROV_ATTRIBUTES = %w(context source license)
+    DCTERMS_ATTRIBUTES = %w(creator created)
+
+    def initialize
+      super
+      self << provenance
+      self << prov_resources
+      self << dcterms_resources
+    end
+
+  private
+
+    def provenance_attributes
+      [
+       #[predicate, object]
+        ['prov:context', 'public'],
+        ['prov:source' , 'https://github.com/petervandenabeele/dbd/blob/d37360070e7f8e61a19c2bca210c881a151ded75/docs/rationale.md'],
+        ['dcterms:creator' , 'Peter Vandenabeele (@peter_v)'],
+        ['dcterms:created', Time.new(2013,5,26,23,30,0,'+02:00').utc],
+        ['prov:license', 'Copyright 2013 Peter Vandenabeele (http://vandenabeele.com), licensed under MIT license.']
+      ]
+    end
+
+    def prov_resources
+      PROV_ATTRIBUTES.map do |attribute|
+        resource = Dbd::Resource.new(provenance_subject: provenance.subject)
+        resource << fact_defines_predicate_prov(attribute)
+        resource << fact_label(attribute)
+      end
+    end
+
+    # NOTE using dcterms:creator is not exact for now as the range
+    #      should be a dcterms:Agent and it is a Literal here.
+    def dcterms_resources
+      DCTERMS_ATTRIBUTES.map do |attribute|
+        resource = Dbd::Resource.new(provenance_subject: provenance.subject)
+        resource << fact_defines_predicate_dcterms(attribute)
+        resource << fact_label(attribute)
+      end
+    end
+
+    def fact_defines_predicate_prov(attribute)
+      Dbd::Fact.new(predicate: 'meta:defines_predicate', object: "prov:#{attribute}")
+    end
+
+    def fact_defines_predicate_dcterms(attribute)
+      Dbd::Fact.new(predicate: 'meta:defines_predicate', object: "dcterms:#{attribute}")
+    end
+
+  end
+end

data/lib/dbd_onto/provenance_methods.rb

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+module DbdOnto
+  module ProvenanceMethods
+
+    def provenance
+      # memoize to avoid making new_provenance on each call
+      @provenance ||= new_provenance
+    end
+
+    def new_provenance
+      Dbd::ProvenanceResource.new.tap do |_provenance|
+        provenance_attributes.each do |provenance_fact_data|
+          _provenance << provenance_fact(provenance_fact_data)
+        end
+      end
+    end
+
+    def provenance_fact(provenance_fact_data)
+      Dbd::ProvenanceFact.new(
+        predicate: provenance_fact_data.first,
+        object: provenance_fact_data.last)
+    end
+
+  end
+end

data/lib/dbd_onto/version.rb

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+module DbdOnto
+  VERSION = "0.0.1"
+end

data/lib/dbd_onto.rb

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+require 'dbd'
+require 'dbd_onto/provenance_methods'
+require 'dbd_onto/fact_methods'
+require 'dbd_onto/version'
+require 'dbd_onto/base'
+require 'dbd_onto/provenance'
+require 'dbd_onto/meta'

data/spec/lib/dbd_onto/base_spec.rb

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+require 'spec_helper'
+
+describe DbdOnto::Base do
+
+  it "is a Dbd::Graph" do
+    subject.should be_a(Dbd::Graph)
+  end
+
+end

data/spec/lib/dbd_onto/meta_spec.rb

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+require 'spec_helper'
+
+describe DbdOnto::Meta do
+
+  it "is a Dbd::Graph" do
+    subject.should be_a(Dbd::Graph)
+  end
+
+  it "all facts in the provenance ontology have a provenance with context public" do
+    subject.all? do |fact|
+      fact.is_a?(Dbd::ProvenanceFact) ||
+        check_provenance?(subject.by_subject(fact.provenance_subject))
+    end.should be_true
+  end
+
+  def check_provenance?(provenance_facts)
+    provenance_facts.detect {|p| p.predicate == 'prov:context' && p.object == 'public'} &&
+    provenance_facts.detect {|p| p.predicate == 'prov:source'} &&
+    provenance_facts.detect {|p| p.predicate == 'dcterms:creator'} &&
+    provenance_facts.detect {|p| p.predicate == 'dcterms:created'} &&
+    provenance_facts.detect {|p| p.predicate == 'prov:license'}
+  end
+
+  describe "properties include" do
+
+    let(:meta_defines_predicate_subject) do
+      subject.detect do |fact|
+        fact.predicate == 'meta:defines_predicate' &&
+        fact.object == 'meta:defines_predicate'
+      end.subject
+    end
+
+    describe "meta:defines_predicate" do
+
+      let(:defines_predicate_facts) { subject.by_subject(meta_defines_predicate_subject) }
+
+      it "defines the predicate meta:defines_predicate" do
+        meta_defines_predicate_subject.should_not be_nil
+      end
+
+      it "has label 'Defines predicate'" do
+        defines_predicate_facts.detect do |fact|
+          fact.predicate == 'rdfs:label' &&
+          fact.object == 'Defines predicate'
+        end.should_not be_nil
+      end
+    end
+  end
+end

data/spec/lib/dbd_onto/provenance_spec.rb

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+require 'spec_helper'
+
+describe DbdOnto::Provenance do
+
+  it "is a Dbd::Graph" do
+    subject.should be_a(Dbd::Graph)
+  end
+
+  it "all facts in the provenance ontology have a provenance with context public" do
+    subject.all? do |fact|
+      fact.is_a?(Dbd::ProvenanceFact) ||
+        check_provenance?(subject.by_subject(fact.provenance_subject))
+    end.should be_true
+  end
+
+  def check_provenance?(provenance_facts)
+    provenance_facts.detect {|p| p.predicate == 'prov:context' && p.object == 'public'} &&
+    provenance_facts.detect {|p| p.predicate == 'prov:source'} &&
+    provenance_facts.detect {|p| p.predicate == 'dcterms:creator'} &&
+    provenance_facts.detect {|p| p.predicate == 'dcterms:created'} &&
+    provenance_facts.detect {|p| p.predicate == 'prov:license'}
+  end
+
+  describe "properties include" do
+
+    let(:context_subject) do
+      subject.detect do |fact|
+        fact.predicate == 'meta:defines_predicate' &&
+        fact.object == 'prov:context'
+      end.subject
+    end
+
+    let(:source_subject) do
+      subject.detect do |fact|
+        fact.predicate == 'meta:defines_predicate' &&
+        fact.object == 'prov:source'
+      end.subject
+    end
+
+    describe "prov:subject and prov:source" do
+      it "are different subjects" do
+        context_subject.should_not == source_subject
+      end
+    end
+
+    describe "prov:context" do
+
+      let(:context_facts) { subject.by_subject(context_subject) }
+
+      it "defines the predicate prov:context" do
+        context_subject.should_not be_nil
+      end
+
+      it "has label Context" do
+        context_facts.detect do |fact|
+          fact.predicate == 'rdfs:label' &&
+          fact.object == 'Context'
+        end.should_not be_nil
+      end
+    end
+
+    describe "prov:source" do
+
+      let(:source_facts) { subject.by_subject(source_subject) }
+
+      it "defines the predicate prov:source" do
+        source_subject.should_not be_nil
+      end
+
+      it "has label Source" do
+        source_facts.detect do |fact|
+          fact.predicate == 'rdfs:label' &&
+          fact.object == 'Source'
+        end.should_not be_nil
+      end
+    end
+
+    describe "dcterms:creator" do
+      it "defines the predicate" do
+        subject.detect do |fact|
+          fact.predicate == 'meta:defines_predicate' &&
+          fact.object == 'dcterms:creator'
+        end.should_not be_nil
+      end
+    end
+
+    describe "dcterms:created" do
+      it "defines the predicate" do
+        subject.detect do |fact|
+          fact.predicate == 'meta:defines_predicate' &&
+          fact.object == 'dcterms:created'
+        end.should_not be_nil
+      end
+    end
+
+    describe "prov:license" do
+      it "defines the predicate" do
+        subject.detect do |fact|
+          fact.predicate == 'meta:defines_predicate' &&
+          fact.object == 'prov:license'
+        end.should_not be_nil
+      end
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,11 @@
+require 'dbd_onto'
+
+RSpec.configure do |config|
+  config.treat_symbols_as_metadata_keys_with_true_values = true
+
+  # Run specs in random order to surface order dependencies. If you find an
+  # order dependency and want to debug it, you can fix the order by providing
+  # the seed, which is printed after each run.
+  #     --seed 1234
+  config.order = 'random'
+end

metadata

@@ -0,0 +1,183 @@
+--- !ruby/object:Gem::Specification
+name: dbd_onto
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Peter Vandenabeele
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-06-03 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.2.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.2.4
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: guard-rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: terminal-notifier-guard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdf
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.6
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.6
+- !ruby/object:Gem::Dependency
+  name: ruby_peter_v
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.8
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.8
+- !ruby/object:Gem::Dependency
+  name: dbd
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.5
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.5
+description: Ontologies for Dbd
+email:
+- peter@vandenabeele.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- .rspec
+- .rvmrc
+- .travis.yml
+- Gemfile
+- Guardfile
+- HISTORY.txt
+- LICENSE.txt
+- README.md
+- Rakefile
+- dbd_onto.gemspec
+- lib/dbd_onto.rb
+- lib/dbd_onto/base.rb
+- lib/dbd_onto/fact_methods.rb
+- lib/dbd_onto/meta.rb
+- lib/dbd_onto/provenance.rb
+- lib/dbd_onto/provenance_methods.rb
+- lib/dbd_onto/version.rb
+- spec/lib/dbd_onto/base_spec.rb
+- spec/lib/dbd_onto/meta_spec.rb
+- spec/lib/dbd_onto/provenance_spec.rb
+- spec/spec_helper.rb
+homepage: ''
+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: 2.0.3
+signing_key: 
+specification_version: 4
+summary: Ontologies for Dbd
+test_files:
+- spec/lib/dbd_onto/base_spec.rb
+- spec/lib/dbd_onto/meta_spec.rb
+- spec/lib/dbd_onto/provenance_spec.rb
+- spec/spec_helper.rb
+has_rdoc: