bio-sparql-client 0.0.1

data/lib/bio-sparql-client.rb

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+# Bio-SPARQL-client
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol@chalmers.se>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+
+$: << File.join(File.expand_path(File.dirname(__FILE__)))
+
+#Internal library
+require 'open-uri'
+require 'json'
+require 'i18n'
+
+#External library
+#require 'bio-vcf'
+require 'bio'
+require 'sparql'
+require 'sparql/client'
+
+
+require 'bio-sparql-client/term.rb'
+require 'bio-sparql-client/chembl.rb'
+require 'bio-sparql-client/reactome.rb'
+require 'bio-sparql-client/uniprot.rb'
+require 'bio-sparql-client/kegg.rb'
+require 'bio-sparql-client/identifiers.rb'
+require 'bio-sparql-client/bioportal.rb'
+
+I18n.enforce_available_locales = false
+
+#library
+
+module BSPARQLCLI
+    
+end

data/lib/bio-sparql-client/addon.rb

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+# 
+# Exodus
+# Copyright (C) 2014
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+require 'exodb/addon/string.rb'
+

data/lib/bio-sparql-client/addon/string.rb

@@ -0,0 +1,26 @@
+# 
+# Exodus
+# Copyright (C) 2014
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+class String
+	
+	def is_miriam?
+		return self =~ /^urn:miriam:/
+	end
+	
+	def id
+		return self.is_miriam? ? self.split(':', 4)[-1] : ''
+	end
+	
+	def namespace
+		return self.is_miriam? ? self.split(':', 4)[2] : ''
+	end
+	
+end

data/lib/bio-sparql-client/bioportal.rb

@@ -0,0 +1,33 @@
+# Bio-SPARQL-client
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol@chalmers.se>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+module BSPARQLCLI
+    
+    class BioPortal < SPARQL::Client
+        
+        ENDPOINT = 'http://sparql.bioontology.org'
+        
+        def initialize()
+            super(ENDPOINT)
+        end
+        
+    end
+end
+
+#sparql = BSPARQLCLI::BioPortal.new()
+#query = sparql.select(:vrtID, :graph).distinct.where(
+#    [:vrtID, RDF::META['hasVersion'], :version],
+#    [:version, RDF::META['hasDataGraph'], :graph]
+#).limit(10)
+#
+#puts query.inspect
+#
+#query.each_solution do |solution|
+#  puts solution.inspect
+#end

data/lib/bio-sparql-client/chembl.rb

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+# Bio-SPARQL-client
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol@chalmers.se>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+module BSPARQLCLI
+    
+    class ChEMBL < SPARQL::Client
+        
+        ENDPOINT = 'http://www.ebi.ac.uk/rdf/services/chembl/sparql'
+        
+        def initialize()
+            super(ENDPOINT)
+        end
+        
+    end
+end
+
+#sparql = BSPARQLCLI::ChEMBL.new()
+##query = sparql.select(:molecule).where([:molecule, 'a', :type], [:type, 'rdfs:subClassOf*', 'cco:Substance']).prefix('rdfs: <http://www.w3.org/2000/01/rdf-schema#>').prefix('cco: <http://rdf.ebi.ac.uk/terms/chembl#>').offset(100).limit(10)
+#query = sparql.select(:molecule).where([:molecule, 'a', :type], [:type, RDF::RDFS['subClassOf'], BSPARQLCLI::ChEMBL::CCO['Substance']]).limit(10)
+#
+#query.each_solution do |solution|
+#  puts solution.inspect
+#end
+

data/lib/bio-sparql-client/exception.rb

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+# 
+# Exodus
+# Copyright (C) 2014
+#
+# author: Natapol Pornputtapong <natapol.por@gmail.com>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+# raise "Please, use ruby 1.9.0 or later." if RUBY_VERSION < "1.9.0"
+
+module Dactyls
+
+	class CreateUserError < Exception
+		
+	end
+
+end

data/lib/bio-sparql-client/identifiers.rb

@@ -0,0 +1,34 @@
+# Bio-SPARQL-client
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol@chalmers.se>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+module BSPARQLCLI
+    
+    class Identifiers < SPARQL::Client
+        
+        ENDPOINT = 'http://identifiers.org/services/sparql'
+        
+        def initialize()
+            super(ENDPOINT)
+        end
+        
+    end
+end
+
+#sparql = BSPARQLCLI::Identifiers.new()
+#query = sparql.select(:species, :go_term, :go_description).distinct.where(
+#    [:model, RDF::SBMLRDF['species'], :s],
+#    [:s, RDF::SBMLRDF['name'], :species],
+#    [:s, RDF::BQBIO['isVersionOf'], :go_term],
+#).filter(:model == 'biomodel:BIOMD0000000001').limit(10)
+#
+#puts query.inspect
+#
+#query.each_solution do |solution|
+#  puts solution.inspect
+#end

data/lib/bio-sparql-client/kegg.rb

@@ -0,0 +1,32 @@
+# Bio-SPARQL-client
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol@chalmers.se>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+module BSPARQLCLI
+    
+    class KEGG < SPARQL::Client
+        
+        ENDPOINT = 'http://www.genome.jp/sparql/linkdb'
+        
+        def initialize()
+            super(ENDPOINT)
+        end
+        
+    end
+end
+
+#sparql = BSPARQLCLI::KEGG.new()
+#query = sparql.select().where(
+#    [:s, :p, :o]
+#).limit(10)
+#
+#puts query.inspect
+#
+#query.each_solution do |solution|
+#  puts solution.inspect
+#end

data/lib/bio-sparql-client/reactome.rb

@@ -0,0 +1,34 @@
+# Bio-SPARQL-client
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol@chalmers.se>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+module BSPARQLCLI
+    
+    class Reactome < SPARQL::Client
+        
+        ENDPOINT = 'http://www.ebi.ac.uk/rdf/services/reactome/sparql'
+        
+        def initialize()
+            super(ENDPOINT)
+        end
+        
+    end
+end
+
+#sparql = BSPARQLCLI::Reactome.new()
+#query = sparql.select(:pathway, :pathwayname).distinct().where(
+#    [:pathway, RDF::RDF22['type'], RDF::BIOPAX3['Pathway']],
+#    [:pathway, RDF::BIOPAX3['displayName'], :pathwayname],
+#    [:pathway, RDF::BIOPAX3['organism'], RDF::URI.new("http://identifiers.org/taxonomy/9606")]
+#).limit(10)
+#
+#puts query.inspect
+#
+#query.each_solution do |solution|
+#  puts solution.inspect
+#end

data/lib/bio-sparql-client/term.rb

@@ -0,0 +1,70 @@
+# Bio-SPARQL-client
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol@chalmers.se>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+module RDF
+	
+	#EMBL prefix
+	RDF22 = RDF::Vocabulary.new("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
+	DCTERMS = RDF::Vocabulary.new("http://purl.org/dc/terms/")
+	BIOPAX3 = RDF::Vocabulary.new("http://www.biopax.org/release/biopax-level3.owl#")
+    CCO = RDF::Vocabulary.new("http://rdf.ebi.ac.uk/terms/chembl#")
+    VOID = RDF::Vocabulary.new("http://rdfs.org/ns/void#")
+	PAV = RDF::Vocabulary.new("http://purl.org/pav/2.0/")
+	OBO = RDF::Vocabulary.new("http://purl.obolibrary.org/obo/")
+	SIO = RDF::Vocabulary.new("http://semanticscience.org/resource/")
+	EFO = RDF::Vocabulary.new("http://www.ebi.ac.uk/efo/")
+	ATLAS = RDF::Vocabulary.new("http://rdf.ebi.ac.uk/resource/atlas/")
+	ATLASTERMS = RDF::Vocabulary.new("http://rdf.ebi.ac.uk/terms/atlas/")
+	SBMLRDF = RDF::Vocabulary.new("http://identifiers.org/biomodels.vocabulary#")
+    BQBIO = RDF::Vocabulary.new("http://biomodels.net/biology-qualifiers#")
+    BIOMODEL = RDF::Vocabulary.new("http://identifiers.org/biomodels.db/")
+    
+	#UNIPROT
+	FALDO = RDF::Vocabulary.new("http://biohackathon.org/resource/faldo#")
+	UP = RDF::Vocabulary.new("http://purl.uniprot.org/core/")
+	TAXON = RDF::Vocabulary.new("http://purl.uniprot.org/taxonomy/")
+	KEYWORDS = RDF::Vocabulary.new("http://purl.uniprot.org/keywords/")
+	UNIPROTKB = RDF::Vocabulary.new("http://purl.uniprot.org/uniprot/")
+	EC = RDF::Vocabulary.new("http://purl.uniprot.org/enzyme/")
+	BIBO = RDF::Vocabulary.new("http://purl.org/ontology/bibo/")
+	
+	#BioPortal
+	META = RDF::Vocabulary.new("http://bioportal.bioontology.org/metadata/def/")
+	
+	#KEGG
+	#bif	bif:
+	#dawgt	http://www.w3.org/2001/sw/DataAccess/tests/test-dawg#
+	#dbpedia	http://dbpedia.org/resource/
+	#dbpprop	http://dbpedia.org/property/
+	#fn	http://www.w3.org/2005/xpath-functions/#
+	#go	http://purl.org/obo/owl/GO#
+	#math	http://www.w3.org/2000/10/swap/math#
+	#mesh	http://purl.org/commons/record/mesh/
+	#mf	http://www.w3.org/2001/sw/DataAccess/tests/test-manifest#
+	#nci	http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
+	#obo	http://www.geneontology.org/formats/oboInOwl#
+	#product	http://www.buy.com/rss/module/productV2/
+	#protseq	http://purl.org/science/protein/bysequence/
+	#rdfa	http://www.w3.org/ns/rdfa#
+	#rdfdf	http://www.openlinksw.com/virtrdf-data-formats#
+	#sc	http://purl.org/science/owl/sciencecommons/
+	#scovo	http://purl.org/NET/scovo#
+	#sd	http://www.w3.org/ns/sparql-service-description#
+	#sql	sql:
+	#vcard2006	http://www.w3.org/2006/vcard/ns#
+	#virtcxml	http://www.openlinksw.com/schemas/virtcxml#
+	#virtrdf	http://www.openlinksw.com/schemas/virtrdf#
+	#xf	http://www.w3.org/2004/07/xpath-functions
+	#xml	http://www.w3.org/XML/1998/namespace
+	#xsl10	http://www.w3.org/XSL/Transform/1.0
+	#xsl1999	http://www.w3.org/1999/XSL/Transform
+	#xslwd	http://www.w3.org/TR/WD-xsl
+	#yago	http://dbpedia.org/class/yago/
+	
+end

data/lib/bio-sparql-client/uniprot.rb

@@ -0,0 +1,34 @@
+# Bio-SPARQL-client
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol@chalmers.se>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+module BSPARQLCLI
+    
+    class UniProt < SPARQL::Client
+        
+        ENDPOINT = 'http://beta.sparql.uniprot.org/sparql'
+        
+        def initialize()
+            super(ENDPOINT)
+        end
+        
+    end
+end
+
+#sparql = BSPARQLCLI::UniProt.new()
+#query = sparql.select(:taxon, :name).where(
+#    [:taxon, 'a', RDF::UP['Taxon']],
+#    [:taxon, RDF::UP['scientificName'], :name],
+#    [:taxon, RDF::RDFS['subClassOf'], RDF::TAXON['2']]
+#).limit(10)
+#
+#puts query.inspect
+#
+#query.each_solution do |solution|
+#  puts solution.inspect
+#end

data/lib/bio-sparql-client/version.rb

@@ -0,0 +1,12 @@
+# Bio-SPARQL-client
+# 
+# Copyright (C) 2015
+#
+# author: Natapol Pornputtapong <natapol@chalmers.se>
+#
+# Documentation: Natapol Pornputtapong (RDoc'd and embellished by William Webber)
+#
+
+module BSPARQLCLI
+    VERSION = "0.0.1"
+end

metadata

@@ -0,0 +1,77 @@
+--- !ruby/object:Gem::Specification
+name: bio-sparql-client
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Natapol Pornputtapong
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-04-24 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: sparql-client
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.1'
+description: A ruby wrapper for bio SPARQL service
+email:
+- natapol.por@gmail.com
+- natapol.pornputtapong@yale.edu
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- LICENSE
+- README.md
+- Rakefile
+- bio-sparql-client.gemspec
+- error
+- lib/bio-sparql-client.rb
+- lib/bio-sparql-client/addon.rb
+- lib/bio-sparql-client/addon/string.rb
+- lib/bio-sparql-client/bioportal.rb
+- lib/bio-sparql-client/chembl.rb
+- lib/bio-sparql-client/exception.rb
+- lib/bio-sparql-client/identifiers.rb
+- lib/bio-sparql-client/kegg.rb
+- lib/bio-sparql-client/reactome.rb
+- lib/bio-sparql-client/term.rb
+- lib/bio-sparql-client/uniprot.rb
+- lib/bio-sparql-client/version.rb
+homepage: http://rubygems.org/gems/bio-sparql-client
+licenses:
+- GPL-3.0
+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: 2.0.14
+signing_key: 
+specification_version: 4
+summary: A ruby wrapper for bio SPARQL service
+test_files: []
+has_rdoc: