bel 0.6.0 → 0.7.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: e13d38c9a6775f28b83bd6803f076dec155feb30
+  metadata.gz: f60c8d511672752ce1913092b9c8f11bce1afcf7
+  data.tar.gz: 7af3edc1edfb6d481168297a4799af8c7c9e0128
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+  data.tar.gz: f10f81d5c54a55d2c359c30b62af642de45ff3b479db9b81f096def42c881abd76271efe5b00dfbbfec862805fea34111ffb22634a6a337703076eba729008eb

data/CHANGELOG.md

@@ -3,6 +3,14 @@ All notable changes to bel.rb will be documented in this file. The curated log b
 
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.7.0][0.7.0] - 2016-04-12
+### Fixed
+- RDF translation allows for RDF prefixes to be used. Default RDF prefixes are provided ([Issue #69][69]).
+
+### Added
+- Annotation and Namespace definitions can now be remapped using a YAML file ([Issue #92][92]).
+- An example remap file can be obtained from the command `bel remapfile` ([Issue #92][92]).
+
 ## [0.6.0][0.6.0] - 2016-03-15
 ### Fixed
 - Serialization of BEL Script / XBEL can produce incorrect annotation and namespaces references ([Issue #111][111]).
@@ -91,6 +99,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ### Added
 - Development gem dependencies (i.e. byebug, pry, pry-byebug) for debugging.
 
+[0.7.0]:    https://github.com/OpenBEL/bel.rb/compare/0.6.0...0.7.0
 [0.6.0]:    https://github.com/OpenBEL/bel.rb/compare/0.5.0...0.6.0
 [0.5.0]:    https://github.com/OpenBEL/bel.rb/compare/0.4.2...0.5.0
 [0.4.2]:    https://github.com/OpenBEL/bel.rb/compare/0.4.1...0.4.2
@@ -108,12 +117,14 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 [64]:       https://github.com/OpenBEL/bel.rb/issues/64
 [66]:       https://github.com/OpenBEL/bel.rb/issues/66
 [68]:       https://github.com/OpenBEL/bel.rb/issues/68
+[69]:       https://github.com/OpenBEL/bel.rb/issues/69
 [71]:       https://github.com/OpenBEL/bel.rb/issues/71
 [82]:       https://github.com/OpenBEL/bel.rb/issues/82
 [85]:       https://github.com/OpenBEL/bel.rb/issues/85
 [86]:       https://github.com/OpenBEL/bel.rb/pull/86
 [90]:       https://github.com/OpenBEL/bel.rb/issues/90
 [91]:       https://github.com/OpenBEL/bel.rb/issues/91
+[92]:       https://github.com/OpenBEL/bel.rb/issues/92
 [93]:       https://github.com/OpenBEL/bel.rb/issues/93
 [94]:       https://github.com/OpenBEL/bel.rb/issues/94
 [95]:       https://github.com/OpenBEL/bel.rb/issues/95

data/README.md

@@ -71,7 +71,6 @@ the root of the bel.rb tree:
     export BR_ISOLATE="yes"
 ```
 
-
 ## branches
 
 - master branch
@@ -108,10 +107,12 @@ the root of the bel.rb tree:
       translate
       upgrade
       plugins
+      generate
+      remapfile
 
 
     bel
-    Copyright (C) 2015 OpenBEL
+    Copyright (C) 2016 OpenBEL
     Apache License, Version 2.0, January 2004
     http://www.apache.org/licenses/
 
@@ -121,7 +122,6 @@ the root of the bel.rb tree:
       -h, --help       Show this message
 ```
 
-
 **bel2rdf.rb**: Converts BEL to RDF.
 
 ```bash

data/bel.gemspec

@@ -26,6 +26,7 @@ Gem::Specification.new do |spec|
                                   ]
   spec.files                    = [
                                     Dir.glob('lib/**/*.rb'),
+                                    Dir.glob('lib/**/*.yml'),
                                     Dir.glob('ext/**/*.{c,h,def}'),
                                     Dir.glob('lib/bel/libbel/ext/{java,mingw}/**/*.{so,bundle}'),
                                     __FILE__,

data/bin/bel

@@ -7,7 +7,7 @@ require 'bel/vendor/trollop'
 
 VERSION_BANNER = <<-VERSION
 bel #{BEL::VERSION}
-Copyright (C) 2015 OpenBEL
+Copyright (C) #{Time.now.year} OpenBEL
 Apache License, Version 2.0, January 2004
 http://www.apache.org/licenses/
 VERSION
@@ -64,27 +64,41 @@ Subcommands:
             synopsis "Converts BEL to RDF."
             usage    "[OPTIONS]... bel2rdf [OPTIONS]"
 
-            opt      :bel,       'The BEL script to parse and output (Defaults to STDIN).',
-                     :type    => String,
-                     :long    => :bel,
-                     :short   => :b,
-                     :default => nil
-
-            opt      :format,    'The RDF format to output.',
-                     :type    => String,
-                     :long    => :format,
-                     :short   => :f,
-                     :default => 'ntriples'
-
-            opt      :schema,    'Includes the BEL RDFS schema in RDF output.',
-                     :long    => :schema,
-                     :short   => :s,
-                     :default => false
+            opt      :bel,                 'The BEL script to parse and output (Defaults to STDIN).',
+                     :type              => String,
+                     :long              => :bel,
+                     :short             => :b,
+                     :default           => nil
+
+            opt      :format,              'The RDF format to output.',
+                     :type              => String,
+                     :long              => :format,
+                     :short             => :f,
+                     :default           => 'ntriples'
+
+            opt      :schema,              'Includes the BEL RDFS schema in RDF output.',
+                     :long              => :schema,
+                     :short             => :s,
+                     :default           => false
+
+            opt      :'rdf-prefix-file',   "A YAML file mapping prefix containing key/value pairs. The key is an RDF prefix to use in the RDF output; the value is the RDF URI for that prefix. For example, belv: 'http://www.openbel.org/vocabulary/'",
+                     :type              => String,
+                     :long              => :'rdf-prefix-file',
+                     :short             => :p,
+                     :default           => nil
+
+            opt      :'remap-file',        'A YAML file that remaps annotation and namespace definitions. Run "bel remapfile" to get an example of the YAML format.',
+                     :type              => String,
+                     :long              => :'remap-file',
+                     :short             => :r,
+                     :default           => nil
           end
 
-        ARGV.concat(['--bel',    parsed_options[:bel]])    if parsed_options[:bel]
-        ARGV.concat(['--format', parsed_options[:format]]) if parsed_options[:format]
-        ARGV.concat(['--schema', parsed_options[:schema]]) if parsed_options[:schema]
+        ARGV.concat(['--bel',             parsed_options[:bel]])               if parsed_options[:bel]
+        ARGV.concat(['--format',          parsed_options[:format]])            if parsed_options[:format]
+        ARGV.concat(['--schema',          parsed_options[:schema]])            if parsed_options[:schema]
+        ARGV.concat(['--rdf-prefix-file', parsed_options[:'rdf-prefix-file']]) if parsed_options[:'rdf-prefix-file']
+        ARGV.concat(['--remap-file',      parsed_options[:'remap-file']])      if parsed_options[:'remap-file']
 
         require_relative 'bel2rdf'
       end
@@ -234,7 +248,32 @@ Subcommands:
         parsed_options =
           Trollop::options do
             synopsis "Translates BEL evidence between formats using translator plugins."
-            usage    "[OPTIONS]... translate [OPTIONS] FROM_TRANSLATOR TO_TRANSLATOR"
+            usage    <<-DOC.gsub(/^ {14}/, '')
+              [OPTIONS]... translate [OPTIONS] FROM_TRANSLATOR TO_TRANSLATOR
+
+              From options:
+                None
+              To options:
+                streaming=true|false
+                  Set to "true" to enable streaming writes for translators that support it.
+                  Set to "false" to disable streaming.
+                serialization=discrete|topdown|citation [BEL Script translator]
+                  Set to "discrete" to render each statement with its annotations.
+                  Set to "topdown" to set/unset annotations as needed.
+                  Set to "citation" to use statement groups for each citation.
+                write_schema=true|false
+                  Set to "true" to write RDFS schema for RDF-based translators.
+                  Set to "false" to omit RDFS schema for RDF-based translators.
+                void_dataset_uri=URI
+                  The VoID dataset URI to use for the dataset of an RDF-based translation.
+                rdf_prefix_file=FILE
+                  A YAML file mapping prefix containing key/value pairs. The key is an
+                  RDF prefix to use in the RDF output; the value is the RDF URI for that
+                  prefix. For example, belv: 'http://www.openbel.org/vocabulary/'.
+                remap_file=FILE
+                  A YAML file that remaps annotation and namespace definitions.
+                  Run "bel remapfile" to get an example of the YAML format.
+            DOC
 
             opt      :'input-file', 'The file containing evidence data to translate. If not specified the default is to read from STDIN.',
                      :type    => String,
@@ -297,8 +336,10 @@ Subcommands:
           Trollop::educate
         end
 
-        from_options = map_kv_options(parsed_options, :'from-option')
-        to_options   = map_kv_options(parsed_options, :'to-option')
+        # XXX Merge conflicts.
+        options = {}.
+          merge(map_kv_options(parsed_options, :'from-option')).
+          merge(map_kv_options(parsed_options, :'to-option'))
 
         begin
           BEL.translate(
@@ -306,7 +347,7 @@ Subcommands:
             from_format,
             to_format,
             $stdout,
-            from_options.merge(to_options) # XXX Merge conflicts.
+            options
           )
         ensure
           $stdout.close
@@ -490,6 +531,32 @@ Subcommands:
         translator.write(random_data, $stdout)
       end
     end
+
+    class RemapfileCommand
+
+      def initialize(global_options)
+        @global_options = global_options
+      end
+
+      def run
+        options = Trollop::options do
+          synopsis "Writes an example resource remap YAML file."
+          usage    "[OPTIONS]... remapfile [OPTIONS]"
+        end
+
+        example_file_path =
+          File.join(
+            File.expand_path(File.dirname(__FILE__)),
+            '..',
+            'lib',
+            'bel',
+            'examples',
+            'remap-file-example.yml')
+        File.open(example_file_path) do |f|
+          $stdout.write(f.read)
+        end
+      end
+    end
   end
 end
 

data/bin/bel2rdf.rb

@@ -46,15 +46,35 @@ OptionParser.new do |opts|
     options[:format] = format.downcase
   end
 
+
+  opts.on('-p', '--rdf-prefix-file FILE', "A YAML file mapping prefix containing key/value pairs. The key is an RDF prefix to use in the RDF output; the value is the RDF URI for that prefix. For example, belv: 'http://www.openbel.org/vocabulary/'.") do |prefix_file|
+    options[:rdf_prefix_file] = prefix_file
+  end
+
   opts.on('-s', '--[no-]schema', 'Write BEL RDF schema? The default is to include the schema in the output.') do |schema|
     options[:schema] = schema
   end
+
+  opts.on('-r', '--remap-file FILE', 'A YAML file that remaps annotation and namespace definitions. Run "bel remapfile" to get an example of the YAML format.') do |remap_file|
+    options[:remap_file] = remap_file
+  end
 end.parse!
 
 if options[:bel] and not File.exists? options[:bel]
   $stderr.puts "No file for bel, #{options[:bel]}"
   exit 1
 end
+
+if options[:rdf_prefix_file] and not File.exists? options[:rdf_prefix_file]
+  $stderr.puts "No file for rdf_prefix_file, #{options[:rdf_prefix_file]}"
+  exit 1
+end
+
+if options[:remap_file] and not File.exist? options[:remap_file]
+  $stderr.puts "No file for remap_file, #{options[:remap_file]}"
+  exit 1
+end
+
 unless RDF_TRANSLATORS.include? options[:format]
   $stderr.puts "Format must be one of: #{RDF_TRANSLATORS.join(', ')}"
   exit 1
@@ -77,7 +97,7 @@ end
 # read bel content
 input_io =
   if options[:bel]
-    File.open(options[:bel], :external_encoding => 'UTF-8')
+    File.open(options[:bel], external_encoding: 'UTF-8')
   else
     $stdin
   end
@@ -87,7 +107,9 @@ validate_translator!(options[:format])
 begin
   BEL.translate(input_io, :bel, options[:format], $stdout,
     {
-      :write_schema => options[:schema]
+      write_schema:    options[:schema],
+      rdf_prefix_file: options[:rdf_prefix_file],
+      remap_file:      options[:remap_file]
     }
   )
 ensure

data/lib/bel/examples/remap-file-example.yml

@@ -0,0 +1,50 @@
+namespaces:
+  - remap:
+      from:
+        prefix:  "CHEBI"
+        url:     "http://resource.belframework.org/belframework/20131211/namespace/chebi.belns"
+      to:
+        prefix:  "HGNC"
+        url:     "http://resource.belframework.org/belframework/20150611/namespace/hgnc-human-genes.belns"
+        rdf_uri: "http://identifiers.org/hgnc/"
+  - remap:
+      from:
+        prefix:  "EGID"
+        url:     "http://resource.belframework.org/belframework/20150611/namespace/entrez-gene-ids.belns"
+      to:
+        prefix:  "EGID"
+        url:     "http://resource.belframework.org/belframework/20150611/namespace/entrez-gene-ids.belns"
+        rdf_uri: "http://identifiers.org/ncbigene/"
+  - remap:
+      from:
+        prefix:  "MESHD"
+        url:     "http://resource.belframework.org/belframework/20131211/namespace/mesh-diseases.belns"
+      to:
+        prefix:  "MESHD"
+        url:     "http://resource.belframework.org/belframework/20131211/namespace/mesh-diseases.belns"
+        rdf_uri: "http://identifiers.org/meshd/"
+annotations:
+  - remap:
+      from:
+        keyword:  "Anatomy"
+        type:     "url"
+        domain:   "http://resource.belframework.org/belframework/20131211/annotation/anatomy.belanno"
+      to:
+        keyword:  "Anatomy"
+        type:     "url"
+        domain:   "http://resource.belframework.org/belframework/20131211/annotation/anatomy.belanno"
+        rdf_uri:  "http://identifiers.org/anatomy/"
+  - remap:
+      from:
+        keyword:  "TextLocation"
+        type:     "list"
+        domain:
+          - Abstract
+          - Results
+          - Legend
+          - Review
+      to:
+        keyword: "TextLocation"
+        type:    "pattern"
+        domain:  "Value[0-9]+"
+        rdf_uri:  "http://identifiers.org/text-location/"

data/lib/bel/quoting.rb

@@ -176,8 +176,6 @@ module BEL
       }
     end
 
-    ## Deprecated, remove in [0.6.0].
-
     # @deprecated Use {#quote_if_needed} instead. Will be removed in a
     #             future release.
     def ensure_quotes identifier

data/lib/bel/translator/plugins/bel_script/bel_citation_serialization.rb

@@ -42,14 +42,20 @@ module BEL::Translator::Plugins::BelScript::BelCitationSerialization
     current_annotations[:Citation] = citation if citation
     current_annotations[:Evidence] = summary_text if summary_text
 
+    if !evidence.citation.id || evidence.citation.id.empty?
+      citation_id = quote('')
+    else
+      citation_id = quote_if_needed(evidence.citation.id)
+    end
+
     # Reset cumulative annotations if new citation.
     if cumulative_citation == nil
-      bel << %Q{SET STATEMENT_GROUP = #{quote_if_needed(evidence.citation.id)}\n}
+      bel << %Q{SET STATEMENT_GROUP = #{citation_id}\n}
       cumulative_annotations.clear
     elsif evidence.citation != cumulative_citation
       bel << %Q{UNSET STATEMENT_GROUP\n}
       bel << "\n\n"
-      bel << %Q{SET STATEMENT_GROUP = #{quote_if_needed(evidence.citation.id)}\n}
+      bel << %Q{SET STATEMENT_GROUP = #{citation_id}\n}
       cumulative_annotations.clear
     end
 

data/lib/bel/translator/plugins/rdf/config/default_prefixes.yml

@@ -0,0 +1,6 @@
+belr: 'http://www.openbel.org/bel/'
+belv: 'http://www.openbel.org/vocabulary/'
+bele: 'http://www.openbel.org/evidence/'
+pubmed: 'http://bio2rdf.org/pubmed:'
+rdfs: 'http://www.w3.org/2000/01/rdf-schema#'
+rdf: 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'

data/lib/bel/translator/plugins/rdf/monkey_patch.rb

@@ -12,7 +12,9 @@ module BELRDF
     end
 
     def to_rdf_vocabulary
-      ::RDF::Vocabulary.new("#{@rdf_uri}/")
+      uri = @rdf_uri
+      uri << '/' unless uri.end_with?('/')
+      ::RDF::Vocabulary.new(uri)
     end
   end
 
@@ -33,11 +35,27 @@ module BELRDF
       @ns.to_rdf_vocabulary[URI::encode(@value)]
     end
 
-    def to_rdf(graph_name = nil)
+    def to_rdf(graph_name = nil, remap = nil)
       # resolve encoding to make rdf:type assertions
       if !@enc && @ns.is_a?(BEL::Namespace::NamespaceDefinition)
         @enc = @ns[@value].enc
       end
+
+      # update namespace resource
+      if remap && remap['namespaces']
+        ro_ind = remap['namespaces'].index { |mapping|
+          mapping['remap'] && mapping['remap'].is_a?(Hash) &&
+          mapping['remap']['from'] && mapping['remap']['from'].is_a?(Hash) &&
+          mapping['remap']['from']['prefix'] == @ns.prefix.to_s &&
+          mapping['remap']['from']['url'] == @ns.url
+        }
+        if ro_ind
+          @ns.prefix = remap['namespaces'][ro_ind]['remap']['to']['prefix']
+          @ns.url = remap['namespaces'][ro_ind]['remap']['to']['url']
+          @ns.rdf_uri = remap['namespaces'][ro_ind]['remap']['to']['rdf_uri']
+        end
+      end
+
       uri = to_uri
       encodings = ['A'].concat(@enc.to_s.each_char.to_a).uniq
       encodings.map! { |enc| concept_statement(enc, uri, graph_name)}
@@ -94,7 +112,7 @@ module BELRDF
       end
     end
 
-    def to_rdf(graph_name = nil)
+    def to_rdf(graph_name = nil, remap = nil)
       uri = to_uri
       statements = []
 
@@ -133,14 +151,14 @@ module BELRDF
           end
           # link root protein abundance as hasChild
           root_param = @arguments.find{|x| x.is_a? ::BEL::Model::Parameter}
-          (root_id, root_statements) = ::BEL::Model::Term.new(:p, [root_param]).to_rdf(graph_name)
+          (root_id, root_statements) = ::BEL::Model::Term.new(:p, [root_param]).to_rdf(graph_name, remap)
           statements << ::RDF::Statement.new(uri, BELRDF::BELV.hasChild, root_id, :graph_name => graph_name)
           statements.concat(root_statements)
           return [uri, statements]
         elsif @arguments.find{|x| x.is_a? ::BEL::Model::Term and BELRDF::PROTEIN_VARIANT.include? x.fx}
           # link root protein abundance as hasChild
           root_param = @arguments.find{|x| x.is_a? ::BEL::Model::Parameter}
-          (root_id, root_statements) = ::BEL::Model::Term.new(:p, [root_param]).to_rdf(graph_name)
+          (root_id, root_statements) = ::BEL::Model::Term.new(:p, [root_param]).to_rdf(graph_name, remap)
           statements << ::RDF::Statement.new(uri, BELRDF::BELV.hasChild, root_id, :graph_name => graph_name)
           statements.concat(root_statements)
           return [uri, statements]
@@ -151,14 +169,14 @@ module BELRDF
       @arguments.find_all{ |x|
         x.is_a? ::BEL::Model::Parameter and x.ns != nil
       }.each do |param|
-        param_uri, encoding_statements = param.to_rdf(graph_name)
+        param_uri, encoding_statements = param.to_rdf(graph_name, remap)
         statements.concat(encoding_statements)
         statements << ::RDF::Statement.new(uri, BELRDF::BELV.hasConcept, param_uri, :graph_name => graph_name)
       end
 
       # BELRDF::BELV.hasChild]
       @arguments.find_all{|x| x.is_a? ::BEL::Model::Term}.each do |child|
-        (child_id, child_statements) = child.to_rdf(graph_name)
+        (child_id, child_statements) = child.to_rdf(graph_name, remap)
         statements << ::RDF::Statement.new(uri, BELRDF::BELV.hasChild, child_id, :graph_name => graph_name)
         statements.concat(child_statements)
       end
@@ -205,20 +223,20 @@ module BELRDF
       end
     end
 
-    def to_rdf(graph_name = nil)
+    def to_rdf(graph_name = nil, remap = nil)
       uri        = to_uri
       statements = []
 
       case
       when subject_only?
-        (sub_uri, sub_statements) = @subject.to_rdf(graph_name)
+        (sub_uri, sub_statements) = @subject.to_rdf(graph_name, remap)
         statements << ::RDF::Statement(uri, BELRDF::BELV.hasSubject, sub_uri, :graph_name => graph_name)
         statements.concat(sub_statements)
       when simple?
-        (sub_uri, sub_statements) = @subject.to_rdf(graph_name)
+        (sub_uri, sub_statements) = @subject.to_rdf(graph_name, remap)
         statements.concat(sub_statements)
 
-        (obj_uri, obj_statements) = @object.to_rdf(graph_name)
+        (obj_uri, obj_statements) = @object.to_rdf(graph_name, remap)
         statements.concat(obj_statements)
 
         rel = BELRDF::RELATIONSHIP_TYPE[@relationship.to_s]
@@ -226,9 +244,9 @@ module BELRDF
         statements << ::RDF::Statement(uri, BELRDF::BELV.hasObject, obj_uri,   :graph_name => graph_name)
         statements << ::RDF::Statement(uri, BELRDF::BELV.hasRelationship, rel, :graph_name => graph_name)
       when nested?
-        (sub_uri, sub_statements) = @subject.to_rdf(graph_name)
-        (nsub_uri, nsub_statements) = @object.subject.to_rdf(graph_name)
-        (nobj_uri, nobj_statements) = @object.object.to_rdf(graph_name)
+        (sub_uri, sub_statements) = @subject.to_rdf(graph_name, remap)
+        (nsub_uri, nsub_statements) = @object.subject.to_rdf(graph_name, remap)
+        (nobj_uri, nobj_statements) = @object.object.to_rdf(graph_name, remap)
         statements.concat(sub_statements)
         statements.concat(nsub_statements)
         statements.concat(nobj_statements)
@@ -278,8 +296,25 @@ module BELRDF
       @annotations.each do |_, anno|
         name = anno.name.gsub('"', '')
 
-        if BELRDF::const_defined? name
-          annotation_scheme = BELRDF::const_get name
+        # update annotations resource
+        anno_rdf_uri = nil
+        if remap && remap['annotations']
+          ro_ind = remap['annotations'].index { |mapping|
+            mapping['remap'] && mapping['remap'].is_a?(Hash) &&
+            mapping['remap']['from'] && mapping['remap']['from'].is_a?(Hash) &&
+            mapping['remap']['from']['keyword'] == name && (mapping['remap']['from']['type'] == 'url' ||
+            mapping['remap']['from']['type'] == 'list' &&
+            mapping['remap']['from']['domain'] && mapping['remap']['from']['domain'].is_a?(Array) &&
+            mapping['remap']['from']['domain'].include?(anno.value))
+          }
+          if ro_ind
+            anno_rdf_uri = remap['annotations'][ro_ind]['remap']['to']['rdf_uri']
+            anno_rdf_uri << '/' unless anno_rdf_uri.end_with?('/')
+          end
+        end
+
+        if anno_rdf_uri or BELRDF::const_defined? name
+          annotation_scheme = anno_rdf_uri ? anno_rdf_uri : BELRDF::const_get(name)
           [anno.value].flatten.map{|x| x.gsub('"', '')}.each do |val|
             value_uri = BELRDF::RDF::URI(URI.encode(annotation_scheme + val.to_s))
             statements << ::RDF::Statement.new(evidence, BELRDF::BELV.hasAnnotation, value_uri, :graph_name => graph_name)
@@ -307,7 +342,7 @@ module BELRDF
       BELRDF::BELE[BELRDF.generate_uuid]
     end
 
-    def to_rdf
+    def to_rdf(remap = nil)
       uri                       = to_uri
 
       # parse BEL statement if necessary
@@ -316,7 +351,7 @@ module BELRDF
       end
 
       # convert BEL statement to RDF
-      statement_uri, statements = bel_statement.to_rdf(uri)
+      statement_uri, statements = bel_statement.to_rdf(uri, remap)
 
       statements << ::RDF::Statement.new(uri,           BELRDF::RDF.type,          BELRDF::BELV.Evidence, :graph_name => uri)
       statements << ::RDF::Statement.new(statement_uri, BELRDF::BELV.hasEvidence,  uri,                     :graph_name => uri)

data/lib/bel/translator/plugins/rdf/translator.rb

@@ -1,4 +1,6 @@
 require 'rdf'
+require 'pathname'
+require 'yaml'
 
 require_relative 'uuid'
 require_relative 'bel_schema'
@@ -55,6 +57,11 @@ module BELRDF
 
       wrote_dataset = false
 
+      # read remap file
+      if options[:remap_file]
+        remap = YAML::load_file(options[:remap_file])
+      end
+
       rdf_statement_enum = Enumerator.new do |yielder|
         # enumerate BEL schema
         @rdf_schema.each do |schema_statement|
@@ -73,7 +80,7 @@ module BELRDF
             wrote_dataset = true
           end
 
-          evidence_uri, statements = evidence.to_rdf
+          evidence_uri, statements = evidence.to_rdf(remap)
           statements.each do |statement|
             yielder << statement
           end
@@ -94,6 +101,12 @@ module BELRDF
         :stream => true
       )
 
+      # load RDF prefixes
+      prefixes = load_prefixes(options)
+      prefixes.each do |prefix, uri|
+        rdf_writer.prefix prefix.to_sym, RDF::URI(uri)
+      end
+
       rdf_writer.write_prologue
       rdf_statement_enum.each do |statement|
         rdf_writer << statement
@@ -103,5 +116,18 @@ module BELRDF
 
       io
     end
+
+    def load_prefixes(options)
+      prefix_file = options[:rdf_prefix_file] || default_prefix_file
+      YAML::load_file(prefix_file)
+    end
+
+    def default_prefix_file
+      File.join(
+        File.expand_path(File.dirname(__FILE__)),
+        'config',
+        'default_prefixes.yml'
+      )
+    end
   end
 end

data/lib/bel/translator/plugins/xbel/xbel_yielder.rb

@@ -11,6 +11,7 @@ module BEL::Translator::Plugins
 
       def initialize(data, options = {})
         @data                     = data
+        @streaming                = options.fetch(:streaming, false)
         @annotation_reference_map = options.fetch(:annotation_reference_map, nil)
         @namespace_reference_map  = options.fetch(:namespace_reference_map, nil)
       end

data/lib/bel/version.rb

@@ -1,3 +1,3 @@
 module BEL
-  VERSION = '0.6.0'
+  VERSION = '0.7.0'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel
 version: !ruby/object:Gem::Version
-  version: 0.6.0
+  version: 0.7.0
 platform: ruby
 authors:
 - Anthony Bargnesi
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-03-16 00:00:00.000000000 Z
+date: 2016-04-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -94,6 +94,7 @@ files:
 - lib/bel/evidence_model/streaming_evidence_combiner.rb
 - lib/bel/evidence_model/summary_text.rb
 - lib/bel/evidence_model/util.rb
+- lib/bel/examples/remap-file-example.yml
 - lib/bel/gen.rb
 - lib/bel/gen/annotation.rb
 - lib/bel/gen/citation.rb
@@ -172,6 +173,7 @@ files:
 - lib/bel/translator/plugins/nquads.rb
 - lib/bel/translator/plugins/ntriples.rb
 - lib/bel/translator/plugins/rdf/bel_schema.rb
+- lib/bel/translator/plugins/rdf/config/default_prefixes.yml
 - lib/bel/translator/plugins/rdf/graph_translator.rb
 - lib/bel/translator/plugins/rdf/monkey_patch.rb
 - lib/bel/translator/plugins/rdf/reader.rb