biointerchange 0.2.0 → 0.2.1
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- data/README.md +11 -1
- data/VERSION +1 -1
- data/generators/javaify.rb +1 -1
- data/generators/rdfxml.rb +3 -1
- data/lib/biointerchange/core.rb +14 -13
- data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +61 -9
- data/lib/biointerchange/genomics/gff3_reader.rb +5 -1
- data/lib/biointerchange/gff3o.rb +44 -28
- data/lib/biointerchange/gvf1o.rb +63 -31
- data/lib/biointerchange/so.rb +19627 -0
- data/spec/gff3_rdfwriter_spec.rb +1 -1
- data/spec/gvf_rdfwriter_spec.rb +1 -1
- data/supplemental/java/biointerchange/pom.xml +1 -1
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java +97 -63
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java +686 -102
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SO.java +24000 -0
- data/supplemental/python/biointerchange/gff3o.py +85 -57
- data/supplemental/python/biointerchange/gvf1o.py +565 -84
- data/supplemental/python/biointerchange/so.py +19625 -0
- data/supplemental/python/setup.py +2 -2
- metadata +6 -3
data/README.md
CHANGED
@@ -163,7 +163,12 @@ To use the BioInterchange artifact, set-up add the following to your Maven POM f
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</dependency>
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</dependencies>
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-
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+
Current vocabularies:
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+
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+
* Generic Feature Format Version 3 Ontology (GFF3O)
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* Genome Variation Format Version 1 Ontology (GVF1O)
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+
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+
Usage examples of accessing GFF3O's vocabulary:
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package org.biointerchange;
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@@ -270,6 +275,9 @@ Building a new version of the Ruby vocabulary classes for GFF3, SIO, SOFA (requi
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echo -e "module BioInterchange\n" > lib/biointerchange/sio.rb
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ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sio> SIO >> lib/biointerchange/sio.rb
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echo -e "\nend" >> lib/biointerchange/sio.rb
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+
echo -e "module BioInterchange\n" > lib/biointerchange/so.rb
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+
ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-so> SO >> lib/biointerchange/so.rb
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echo -e "\nend" >> lib/biointerchange/so.rb
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echo -e "module BioInterchange\n" > lib/biointerchange/sofa.rb
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ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sofa> SOFA >> lib/biointerchange/sofa.rb
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echo -e "\nend" >> lib/biointerchange/sofa.rb
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@@ -287,6 +295,7 @@ The source-code generation can be skipped, if none of the ontologies that are us
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ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-gff3o> GFF3O | ruby generators/pythonify.rb > supplemental/python/biointerchange/gff3o.py
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ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-gvf1o> GVF1O | ruby generators/pythonify.rb > supplemental/python/biointerchange/gvf1o.py
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ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sio> SIO | ruby generators/pythonify.rb > supplemental/python/biointerchange/sio.py
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+
ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-so> SO | ruby generators/pythonify.rb > supplemental/python/biointerchange/so.py
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ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sofa> SOFA | ruby generators/pythonify.rb > supplemental/python/biointerchange/sofa.py
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curl ftp://ftp.geneontology.org/pub/go/doc/GO.xrf_abbs | ruby generators/GOxrefify.rb | ruby generators/pythonify.rb > supplemental/python/biointerchange/goxref.py
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@@ -308,6 +317,7 @@ The source-code generation can be skipped, if none of the ontologies that are us
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ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-gff3o> GFF3O | ruby generators/javaify.rb > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java
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ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-gvf1o> GVF1O | ruby generators/javaify.rb > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java
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ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sio> SIO | ruby generators/javaify.rb > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SIO.java
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+
ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-so> SO | ruby generators/javaify.rb "http://purl.obolibrary.org/obo/" > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SO.java
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ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sofa> SOFA | ruby generators/javaify.rb "http://purl.obolibrary.org/obo/" > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java
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curl ftp://ftp.geneontology.org/pub/go/doc/GO.xrf_abbs | ruby generators/GOxrefify.rb | ruby generators/javaify.rb > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GOXRef.java
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.2.
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1
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+
0.2.1
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data/generators/javaify.rb
CHANGED
@@ -51,7 +51,7 @@ STDIN.each { |line|
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end
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transduction << " public static #{line.sub('?', '').sub(/self\./, '').sub(/ *def\ /, '')}"
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method_name = transduction.sub(/^.*public static /m, '').sub(/(\(.*)?$/, '')
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-
transduction.sub!("public static #{method_name}", "public static _#{method_name}_") if method_name.match(/^(true|false|class|public|private|static|return|if|while|do|clone|equals|toString|hashCode)$/)
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+
transduction.sub!("public static #{method_name}", "public static _#{method_name}_") if method_name.match(/^(true|false|class|public|private|static|return|if|while|do|clone|equals|toString|hashCode|byte|char|short|int|long|float|double|boolean)$/)
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variables = transduction.scan(/^\s*public static \w+\((.+)\)$/)
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variables = variables[0][0].split(',').map { |variable| variable.strip } if variables.length > 0
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if method_name == 'is_object_property' then
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data/generators/rdfxml.rb
CHANGED
@@ -80,8 +80,10 @@ model.keys.each { |key|
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comment = [ uri, " # #{entry[OBO_DEF].to_s.sub(/^"(.*)" \[(.*)\]$/, '\1 (\2)').gsub(/\n|\r\n/, "\n # ")}\n" ]
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elsif entry[RDF::RDFS.comment] then
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comment = [ uri, " # #{entry[RDF::RDFS.comment].to_s.gsub(/\n|\r\n/, "\n # ")}\n" ]
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else
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+
comment = [ uri, " # -- No comment or description provided. --\n" ]
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end
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-
comments[label_or_synonym] = set | [ comment ]
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+
comments[label_or_synonym] = set | [ comment ]
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set = combined_uris[label_or_synonym]
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set = [] unless set
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data/lib/biointerchange/core.rb
CHANGED
@@ -24,6 +24,7 @@ module BioInterchange
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require 'biointerchange/goxref'
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require 'biointerchange/gvf1o'
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require 'biointerchange/sio'
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+
require 'biointerchange/so'
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require 'biointerchange/sofa'
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# Reader/writer interfaces
|
@@ -89,21 +90,21 @@ module BioInterchange
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begin
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opt = Getopt::Long.getopts(
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["--help", "-h", Getopt::BOOLEAN],
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-
["--debug", "-d", Getopt::BOOLEAN],
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+
["--debug", "-d", Getopt::BOOLEAN], # set debug mode => print stack traces
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["--no_rdf_graph_optimization", "-n", Getopt::BOOLEAN], # set self.skip_rdf_graph to false
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-
["--batchsize", "-b", Getopt::OPTIONAL],
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["--input", "-i", Getopt::REQUIRED],
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-
["--rdf", "-r", Getopt::REQUIRED],
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["--annotate_name", Getopt::OPTIONAL],
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["--annotate_name_id", Getopt::OPTIONAL],
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["--annotate_date", Getopt::OPTIONAL],
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-
["--annotate_version", Getopt::OPTIONAL],
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["--file", "-f", Getopt::OPTIONAL],
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["--out", "-o", Getopt::OPTIONAL],
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["--version", "-v", Getopt::
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["--batchsize", "-b", Getopt::OPTIONAL], # batchsize for readers/writers that support +postpone?+
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["--input", "-i", Getopt::REQUIRED], # input file format
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["--rdf", "-r", Getopt::REQUIRED], # output file format
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["--annotate_name", Getopt::OPTIONAL], # name of resourcce/tool/person
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["--annotate_name_id", Getopt::OPTIONAL], # uri of resource/tool/person
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["--annotate_date", Getopt::OPTIONAL], # date of processing/annotation
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["--annotate_version", Getopt::OPTIONAL], # version number of resource
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["--file", "-f", Getopt::OPTIONAL], # file to read, will read from STDIN if not supplied
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["--out", "-o", Getopt::OPTIONAL], # output file, will out to STDOUT if not supplied
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["--version", "-v", Getopt::BOOLEAN] # output the version number of the gem and exit
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)
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-
if opt['help'] or not opt['input']
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+
if opt['help'] or not (opt['input'] and opt['rdf'] or opt['version']) then
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puts "Usage: ruby #{$0} -i <format> -r <format> [options]"
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puts ''
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puts 'Supported input formats (--input <format>/-i <format>):'
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@@ -154,7 +155,7 @@ module BioInterchange
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# Print version number and exit:
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if opt['version'] then
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-
puts
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+
puts "BioInterchange #{Gem.loaded_specs["biointerchange"].version}"
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exit
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end
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@@ -145,6 +145,7 @@ protected
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return if @landmarks.has_key?(landmark.seqid)
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landmark_uri = RDF::URI.new("#{set_uri.to_s}/landmark/#{landmark.seqid}")
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@landmarks[landmark.seqid] = landmark_uri
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+
graph.insert(RDF::Statement.new(landmark_uri, RDF.type, @base.Landmark))
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graph.insert(RDF::Statement.new(landmark_uri, @base.with_parent([ @base.id ].flatten, @base.landmark_properties)[0], RDF::Literal.new(landmark.seqid)))
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graph.insert(RDF::Statement.new(landmark_uri, @base.with_parent([ @base.start ].flatten, @base.landmark_properties)[0], RDF::Literal.new(landmark.start_coordinate))) if landmark.start_coordinate
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graph.insert(RDF::Statement.new(landmark_uri, @base.with_parent([ @base.end ].flatten, @base.landmark_properties)[0], RDF::Literal.new(landmark.end_coordinate))) if landmark.end_coordinate
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@@ -164,16 +165,29 @@ protected
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graph.insert(RDF::Statement.new(feature_uri, @base.alias, RDF::Literal.new(value)))
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}
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elsif tag == 'Dbxref' then
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-
feature_properties =
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+
feature_properties = nil
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if @base == BioInterchange::GFF3O then
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+
feature_properties = @base.feature_properties.select { |uri| @base.is_datatype_property?(uri) }[0]
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else
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feature_properties = @base.feature_properties.select { |uri| @base.is_object_property?(uri) }[0]
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+
end
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list.each { |value|
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begin
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+
linkout = nil
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+
# First: determine the Dbxref linkout URI as string
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if value.match(/^dbSNP(_\d+)?:rs\d+$/) then
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-
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+
linkout = "http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=#{value.split(/:/)[1].sub(/^rs/, '')}"
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elsif value.match(/^COSMIC(_\d+)?:COSM\d+$/) then
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-
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+
linkout = "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=#{value.split(/:/)[1].sub(/^COSM/, '')}"
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else
|
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abbreviation, id = value.split(':', 2)
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-
|
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+
linkout = BioInterchange::GOXRef.send(BioInterchange.make_safe_label(abbreviation)).to_s + id
|
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+
end
|
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+
# Second, and finally: add a triple to the graph in the right representative format depending on the ontology used
|
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+
if @base == BioInterchange::GFF3O then
|
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+
graph.insert(RDF::Statement.new(feature_uri, @base.with_parent([ @base.dbxref ].flatten, feature_properties)[0], RDF::Literal.new(linkout, :datatype => RDF::XSD.anyURI )))
|
189
|
+
else
|
190
|
+
graph.insert(RDF::Statement.new(feature_uri, @base.with_parent([ @base.dbxref ].flatten, feature_properties)[0], RDF::URI.new(linkout))) if @base == BioInterchange::GVF1O
|
177
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|
end
|
178
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|
rescue NoMethodError
|
179
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|
raise BioInterchange::Exceptions::InputFormatError, 'Attribute Dbxref link-out is not resolvable, i.e. the name cannot be turned into an URL.'
|
@@ -198,12 +212,12 @@ protected
|
|
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|
list.each { |value|
|
199
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|
graph.insert(RDF::Statement.new(feature_uri, @base.note, RDF::Literal.new(value)))
|
200
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|
}
|
201
|
-
elsif tag == 'Ontology_term'
|
215
|
+
elsif tag == 'Ontology_term' then
|
202
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|
list.each { |value|
|
203
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|
# TODO Sanitize values that are either not in GO xrf_abbs or need conversion to match
|
204
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|
# match their associated Ruby method.
|
205
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|
namespace, accession = value.split(/:/, 2)
|
206
|
-
graph.insert(RDF::Statement.new(feature_uri, @base.ontology_term, RDF::
|
220
|
+
graph.insert(RDF::Statement.new(feature_uri, @base.ontology_term, RDF::Literal.new("#{BioInterchange::GOXRef.send(namespace).to_s}#{accession}", :datatype => RDF::XSD.anyURI )))
|
207
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}
|
208
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elsif tag == 'Parent' then
|
209
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|
list.each { |parent_id|
|
@@ -225,6 +239,8 @@ protected
|
|
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|
graph.insert(RDF::Statement.new(target_uri, @base.with_parent([ @base.end ].flatten, target_object_properties)[0], @base.Positive)) if strand and strand == '+'
|
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|
graph.insert(RDF::Statement.new(target_uri, @base.with_parent([ @base.end ].flatten, target_object_properties)[0], @base.Negative)) if strand and strand == '-'
|
227
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|
graph.insert(RDF::Statement.new(feature_uri, @base.target, target_uri))
|
242
|
+
elsif tag == 'Variant_effect' and @base == BioInterchange::GVF1O then
|
243
|
+
serialize_variant_effects(graph, set_uri, feature_uri, list)
|
228
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|
elsif tag == 'Variant_seq' and @base == BioInterchange::GVF1O then
|
229
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|
serialize_variant_seqs(graph, set_uri, feature_uri, list)
|
230
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|
else
|
@@ -331,6 +347,28 @@ protected
|
|
331
347
|
}
|
332
348
|
end
|
333
349
|
|
350
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+
# Serializes a list of variant effects.
|
351
|
+
#
|
352
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+
# +graph+:: RDF graph to which the structured attribute is added
|
353
|
+
# +set_uri+:: the feature set URI to which the feature belongs to
|
354
|
+
# +feature_uri+:: the feature URI to the feature that is annotated with variant data
|
355
|
+
# +list+:: list of variant values
|
356
|
+
def serialize_variant_effects(graph, set_uri, feature_uri, list)
|
357
|
+
list.each_index { |index|
|
358
|
+
effect = list[index]
|
359
|
+
sequence_variant, variant_index, feature_type, feature_ids = effect.split(' ', 4)
|
360
|
+
feature_ids = feature_ids.split(' ')
|
361
|
+
effect_uri = RDF::URI.new("#{feature_uri.to_s}/variant/#{variant_index}/effect/#{index}")
|
362
|
+
serialize_variant_triple(graph, feature_uri, RDF::URI.new("#{feature_uri.to_s}/variant/#{variant_index}"), @base.effect, effect_uri)
|
363
|
+
graph.insert(RDF::Statement.new(effect_uri, RDF.type, @base.Effect))
|
364
|
+
graph.insert(RDF::Statement.new(effect_uri, @base.sequence_variant, BioInterchange::SO.send(BioInterchange.make_safe_label(sequence_variant))))
|
365
|
+
graph.insert(RDF::Statement.new(effect_uri, @base.feature_type, BioInterchange::SO.send(BioInterchange.make_safe_label(feature_type))))
|
366
|
+
feature_ids.each { |feature_id|
|
367
|
+
graph.insert(RDF::Statement.new(effect_uri, @base.feature, RDF::Literal.new(feature_id)))
|
368
|
+
}
|
369
|
+
}
|
370
|
+
end
|
371
|
+
|
334
372
|
# Serializes a list of variant sequences.
|
335
373
|
#
|
336
374
|
# +graph+:: RDF graph to which the structured attribute is added
|
@@ -341,11 +379,25 @@ protected
|
|
341
379
|
list.each_index { |index|
|
342
380
|
value = list[index]
|
343
381
|
variant_uri = RDF::URI.new("#{feature_uri.to_s}/variant/#{index}")
|
344
|
-
graph
|
345
|
-
@variants[variant_uri.to_s] = true
|
346
|
-
graph.insert(RDF::Statement.new(variant_uri, @base.variant_seq, RDF::Literal.new(value)))
|
382
|
+
serialize_variant_triple(graph, feature_uri, variant_uri, @base.variant_seq, RDF::Literal.new(value))
|
347
383
|
}
|
348
384
|
end
|
385
|
+
|
386
|
+
# Adds a variant to the graph; tracks the variant's URI that RDF.type is only written out once.
|
387
|
+
#
|
388
|
+
# +graph+:: RDF graph to which the variant is added
|
389
|
+
# +feature_uri+:: the feature URI to the feature that is annotated with variant data
|
390
|
+
# +variant_uri+:: URI that identifies the feature in question ("subject", if you like)
|
391
|
+
# +predicate+:: predicate that describes the data being serialized
|
392
|
+
# +object+:: data to be serialized
|
393
|
+
def serialize_variant_triple(graph, feature_uri, variant_uri, predicate, object)
|
394
|
+
unless @variants.has_key?(variant_uri.to_s) then
|
395
|
+
graph.insert(RDF::Statement.new(feature_uri, @base.variant, variant_uri))
|
396
|
+
graph.insert(RDF::Statement.new(variant_uri, RDF.type, @base.Variant))
|
397
|
+
end
|
398
|
+
@variants[variant_uri.to_s] = true
|
399
|
+
graph.insert(RDF::Statement.new(variant_uri, predicate, object))
|
400
|
+
end
|
349
401
|
end
|
350
402
|
|
351
403
|
end
|
@@ -97,7 +97,7 @@ protected
|
|
97
97
|
type = BioInterchange::SOFA.send(BioInterchange.make_safe_label(type))
|
98
98
|
end
|
99
99
|
rescue NoMethodError
|
100
|
-
raise BioInterchange::Exceptions::InputFormatError,
|
100
|
+
raise BioInterchange::Exceptions::InputFormatError, "Type of feature is set to an unknown SOFA term: \"#{type}\""
|
101
101
|
end
|
102
102
|
|
103
103
|
# String to numeric value conversions:
|
@@ -166,6 +166,10 @@ protected
|
|
166
166
|
end
|
167
167
|
end
|
168
168
|
|
169
|
+
# Takes a GFF3/GVF attribute string (column 9) and decompose it into key/value pairs, where
|
170
|
+
# values are representing a list for the (possibly) comma separated GFF3/GVF attribute values.
|
171
|
+
#
|
172
|
+
# +attribute_string+:: key/value string (column 9) as seen in a GFF3/GVF file
|
169
173
|
def split_attributes(attribute_string)
|
170
174
|
attributes = {}
|
171
175
|
attribute_string.split(';').map { |assignment| match = assignment.match(/([^=]+)=(.+)/) ; { match[1].strip => match[2].split(',').map { |value| value.strip } } }.map { |hash| hash.each_pair { |tag,list| attributes[tag] = list } }
|
data/lib/biointerchange/gff3o.rb
CHANGED
@@ -9,12 +9,6 @@ class GFF3O
|
|
9
9
|
return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0004')
|
10
10
|
end
|
11
11
|
|
12
|
-
# Type of the feature, which is either an entry the "lite" version of the Sequence Ontology (SOFA) or a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO).
|
13
|
-
# (http://www.biointerchange.org/gff3o#GFF3_0006)
|
14
|
-
def self.type
|
15
|
-
return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0006')
|
16
|
-
end
|
17
|
-
|
18
12
|
# Either:
|
19
13
|
# Strand of the feature.
|
20
14
|
# (http://www.biointerchange.org/gff3o#GFF3_0010)
|
@@ -79,18 +73,6 @@ class GFF3O
|
|
79
73
|
return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') ]
|
80
74
|
end
|
81
75
|
|
82
|
-
# A database cross-reference to associate a sequence alteration to its representation in another database.
|
83
|
-
# (http://www.biointerchange.org/gff3o#GFF3_0034)
|
84
|
-
def self.dbxref
|
85
|
-
return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0034')
|
86
|
-
end
|
87
|
-
|
88
|
-
# A cross-reference to an ontology term that is associated with a feature.
|
89
|
-
# (http://www.biointerchange.org/gff3o#GFF3_0035)
|
90
|
-
def self.ontology_term
|
91
|
-
return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0035')
|
92
|
-
end
|
93
|
-
|
94
76
|
# Identifies the target that the features aligns to.
|
95
77
|
# (http://www.biointerchange.org/gff3o#GFF3_0039)
|
96
78
|
def self.target
|
@@ -125,6 +107,12 @@ class GFF3O
|
|
125
107
|
return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0005')
|
126
108
|
end
|
127
109
|
|
110
|
+
# Type of the feature, which is either an entry the "lite" version of the Sequence Ontology (SOFA) or a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO).
|
111
|
+
# (http://www.biointerchange.org/gff3o#GFF3_0006)
|
112
|
+
def self.type
|
113
|
+
return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0006')
|
114
|
+
end
|
115
|
+
|
128
116
|
# Either:
|
129
117
|
# Start coordinate of the feature on the seqid landmark.
|
130
118
|
# (http://www.biointerchange.org/gff3o#GFF3_0007)
|
@@ -187,6 +175,18 @@ class GFF3O
|
|
187
175
|
return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0029')
|
188
176
|
end
|
189
177
|
|
178
|
+
# A database cross-reference to associate a sequence alteration to its representation in another database.
|
179
|
+
# (http://www.biointerchange.org/gff3o#GFF3_0034)
|
180
|
+
def self.dbxref
|
181
|
+
return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0034')
|
182
|
+
end
|
183
|
+
|
184
|
+
# A cross-reference to an ontology term that is associated with a feature.
|
185
|
+
# (http://www.biointerchange.org/gff3o#GFF3_0035)
|
186
|
+
def self.ontology_term
|
187
|
+
return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0035')
|
188
|
+
end
|
189
|
+
|
190
190
|
# Name of a feature, which can be used for display purposes. The name is not a unique property among features.
|
191
191
|
# (http://www.biointerchange.org/gff3o#GFF3_0036)
|
192
192
|
def self.name
|
@@ -235,6 +235,16 @@ class GFF3O
|
|
235
235
|
return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0053')
|
236
236
|
end
|
237
237
|
|
238
|
+
# Either:
|
239
|
+
# Sequence associated with this feature, if it has been specified using a FASTA string.
|
240
|
+
# (http://www.biointerchange.org/gff3o#GFF3_0057)
|
241
|
+
# Or:
|
242
|
+
# Sequence associated with this feature, if it has been specified using a FASTA string.
|
243
|
+
# (http://www.biointerchange.org/gff3o#GFF3_0058)
|
244
|
+
def self.sequence
|
245
|
+
return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0057'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0058') ]
|
246
|
+
end
|
247
|
+
|
238
248
|
# Set of genomic sequence features, whose identifiers are unique within the set.
|
239
249
|
# (http://www.biointerchange.org/gff3o#GFF3_0001)
|
240
250
|
def self.Set
|
@@ -302,9 +312,6 @@ class GFF3O
|
|
302
312
|
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0004') then
|
303
313
|
return true
|
304
314
|
end
|
305
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0006') then
|
306
|
-
return true
|
307
|
-
end
|
308
315
|
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0010') then
|
309
316
|
return true
|
310
317
|
end
|
@@ -329,12 +336,6 @@ class GFF3O
|
|
329
336
|
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') then
|
330
337
|
return true
|
331
338
|
end
|
332
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0034') then
|
333
|
-
return true
|
334
|
-
end
|
335
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0035') then
|
336
|
-
return true
|
337
|
-
end
|
338
339
|
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0039') then
|
339
340
|
return true
|
340
341
|
end
|
@@ -363,6 +364,9 @@ class GFF3O
|
|
363
364
|
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0005') then
|
364
365
|
return true
|
365
366
|
end
|
367
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0006') then
|
368
|
+
return true
|
369
|
+
end
|
366
370
|
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0007') then
|
367
371
|
return true
|
368
372
|
end
|
@@ -393,6 +397,12 @@ class GFF3O
|
|
393
397
|
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0029') then
|
394
398
|
return true
|
395
399
|
end
|
400
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0034') then
|
401
|
+
return true
|
402
|
+
end
|
403
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0035') then
|
404
|
+
return true
|
405
|
+
end
|
396
406
|
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0036') then
|
397
407
|
return true
|
398
408
|
end
|
@@ -432,6 +442,12 @@ class GFF3O
|
|
432
442
|
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0055') then
|
433
443
|
return true
|
434
444
|
end
|
445
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0057') then
|
446
|
+
return true
|
447
|
+
end
|
448
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0058') then
|
449
|
+
return true
|
450
|
+
end
|
435
451
|
return false
|
436
452
|
end
|
437
453
|
|
@@ -502,7 +518,7 @@ class GFF3O
|
|
502
518
|
end
|
503
519
|
|
504
520
|
private
|
505
|
-
@@parent_properties = { RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0004') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#
|
521
|
+
@@parent_properties = { RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0004') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0010') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0012') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0014') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0015') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0025') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0021') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0023') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0025') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0039') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0045') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0044') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0047') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0050') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0044') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0056') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0025') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0005') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0006') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0007') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0008') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0009') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0011') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0013') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0029') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0022') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0027') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0024') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0027') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0034') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0035') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0036') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0037') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0041') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0040') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0042') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0040') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0043') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0040') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0046') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0048') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0049') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0053') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0052') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0054') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0052') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0055') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0052') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0057') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0058') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0052') }
|
506
522
|
|
507
523
|
end
|
508
524
|
|
data/lib/biointerchange/gvf1o.rb
CHANGED
@@ -12,12 +12,6 @@ class GVF1O
|
|
12
12
|
return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0004'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0072') ]
|
13
13
|
end
|
14
14
|
|
15
|
-
# Type of the feature, which is either an entry the "lite" version of the Sequence Ontology (SOFA) or a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO).
|
16
|
-
# (http://www.biointerchange.org/gvf1o#GVF1_0006)
|
17
|
-
def self.type
|
18
|
-
return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006')
|
19
|
-
end
|
20
|
-
|
21
15
|
# Either:
|
22
16
|
# Strand of the feature.
|
23
17
|
# (http://www.biointerchange.org/gvf1o#GVF1_0010)
|
@@ -108,12 +102,6 @@ class GVF1O
|
|
108
102
|
return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0043')
|
109
103
|
end
|
110
104
|
|
111
|
-
# Features that are affected by this sequence alteration effect.
|
112
|
-
# (http://www.biointerchange.org/gvf1o#GVF1_0044)
|
113
|
-
def self.feature
|
114
|
-
return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044')
|
115
|
-
end
|
116
|
-
|
117
105
|
# A coordinate range for ambiguous start coordinates.
|
118
106
|
# (http://www.biointerchange.org/gvf1o#GVF1_0046)
|
119
107
|
def self.start_range
|
@@ -178,10 +166,14 @@ class GVF1O
|
|
178
166
|
return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') ]
|
179
167
|
end
|
180
168
|
|
181
|
-
#
|
182
|
-
#
|
169
|
+
# Either:
|
170
|
+
# Properties that are directly associated with Effect class instances.
|
171
|
+
# (http://www.biointerchange.org/gvf1o#GVF1_0070)
|
172
|
+
# Or:
|
173
|
+
# Properties that are directly associated with Effect class instances.
|
174
|
+
# (http://www.biointerchange.org/gvf1o#GVF1_0158)
|
183
175
|
def self.effect_properties
|
184
|
-
return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070')
|
176
|
+
return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0158') ]
|
185
177
|
end
|
186
178
|
|
187
179
|
# Either:
|
@@ -220,12 +212,6 @@ class GVF1O
|
|
220
212
|
return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0092') ]
|
221
213
|
end
|
222
214
|
|
223
|
-
# A cross-reference to an ontology term that is associated with a feature.
|
224
|
-
# (http://www.biointerchange.org/gvf1o#GVF1_0096)
|
225
|
-
def self.ontology_term
|
226
|
-
return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0096')
|
227
|
-
end
|
228
|
-
|
229
215
|
# Either:
|
230
216
|
# Properties that are directly associated with TechnologyPlatform class instances.
|
231
217
|
# (http://www.biointerchange.org/gvf1o#GVF1_0102)
|
@@ -341,12 +327,24 @@ class GVF1O
|
|
341
327
|
return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0150')
|
342
328
|
end
|
343
329
|
|
330
|
+
# Identifies the target that the features aligns to.
|
331
|
+
# (http://www.biointerchange.org/gvf1o#GVF1_0155)
|
332
|
+
def self.target
|
333
|
+
return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0155')
|
334
|
+
end
|
335
|
+
|
344
336
|
# A free text qualifier that describes the algorithm or operating procedure that generated this feature. For example, the name of the software that generated this feature or a database name.
|
345
337
|
# (http://www.biointerchange.org/gvf1o#GVF1_0005)
|
346
338
|
def self.source
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347
339
|
return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0005')
|
348
340
|
end
|
349
341
|
|
342
|
+
# Type of the feature, which is either an entry the "lite" version of the Sequence Ontology (SOFA) or a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO).
|
343
|
+
# (http://www.biointerchange.org/gvf1o#GVF1_0006)
|
344
|
+
def self.type
|
345
|
+
return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006')
|
346
|
+
end
|
347
|
+
|
350
348
|
# Either:
|
351
349
|
# Start coordinate of the feature on the seqid landmark.
|
352
350
|
# (http://www.biointerchange.org/gvf1o#GVF1_0007)
|
@@ -459,6 +457,12 @@ class GVF1O
|
|
459
457
|
return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0039')
|
460
458
|
end
|
461
459
|
|
460
|
+
# Features that are affected by this sequence alteration effect. This can be an external feature identifier, such as an Ensembl gene/transcript identifier.
|
461
|
+
# (http://www.biointerchange.org/gvf1o#GVF1_0044)
|
462
|
+
def self.feature
|
463
|
+
return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044')
|
464
|
+
end
|
465
|
+
|
462
466
|
# Either:
|
463
467
|
# Unclear from GVF specification.
|
464
468
|
# (http://www.biointerchange.org/gvf1o#GVF1_0050)
|
@@ -523,6 +527,12 @@ class GVF1O
|
|
523
527
|
return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0093')
|
524
528
|
end
|
525
529
|
|
530
|
+
# A cross-reference to an ontology term that is associated with a feature.
|
531
|
+
# (http://www.biointerchange.org/gvf1o#GVF1_0096)
|
532
|
+
def self.ontology_term
|
533
|
+
return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0096')
|
534
|
+
end
|
535
|
+
|
526
536
|
# An arbitrary comment. Free text.
|
527
537
|
# (http://www.biointerchange.org/gvf1o#GVF1_0105)
|
528
538
|
def self.comment
|
@@ -577,6 +587,16 @@ class GVF1O
|
|
577
587
|
return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0153')
|
578
588
|
end
|
579
589
|
|
590
|
+
# Either:
|
591
|
+
# Sequence associated with this feature, if it has been specified using a FASTA string.
|
592
|
+
# (http://www.biointerchange.org/gvf1o#GVF1_0156)
|
593
|
+
# Or:
|
594
|
+
# Sequence associated with this feature, if it has been specified using a FASTA string.
|
595
|
+
# (http://www.biointerchange.org/gvf1o#GVF1_0157)
|
596
|
+
def self.sequence
|
597
|
+
return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0156'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0157') ]
|
598
|
+
end
|
599
|
+
|
580
600
|
# Set of genomic sequence features, whose identifiers are unique within the set.
|
581
601
|
# (http://www.biointerchange.org/gvf1o#GVF1_0001)
|
582
602
|
def self.Set
|
@@ -824,9 +844,6 @@ class GVF1O
|
|
824
844
|
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0004') then
|
825
845
|
return true
|
826
846
|
end
|
827
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006') then
|
828
|
-
return true
|
829
|
-
end
|
830
847
|
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0010') then
|
831
848
|
return true
|
832
849
|
end
|
@@ -863,9 +880,6 @@ class GVF1O
|
|
863
880
|
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0043') then
|
864
881
|
return true
|
865
882
|
end
|
866
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044') then
|
867
|
-
return true
|
868
|
-
end
|
869
883
|
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0046') then
|
870
884
|
return true
|
871
885
|
end
|
@@ -920,9 +934,6 @@ class GVF1O
|
|
920
934
|
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0091') then
|
921
935
|
return true
|
922
936
|
end
|
923
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0096') then
|
924
|
-
return true
|
925
|
-
end
|
926
937
|
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0102') then
|
927
938
|
return true
|
928
939
|
end
|
@@ -986,6 +997,9 @@ class GVF1O
|
|
986
997
|
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0152') then
|
987
998
|
return true
|
988
999
|
end
|
1000
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0155') then
|
1001
|
+
return true
|
1002
|
+
end
|
989
1003
|
return false
|
990
1004
|
end
|
991
1005
|
|
@@ -996,6 +1010,9 @@ class GVF1O
|
|
996
1010
|
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0005') then
|
997
1011
|
return true
|
998
1012
|
end
|
1013
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006') then
|
1014
|
+
return true
|
1015
|
+
end
|
999
1016
|
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0007') then
|
1000
1017
|
return true
|
1001
1018
|
end
|
@@ -1035,6 +1052,9 @@ class GVF1O
|
|
1035
1052
|
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0039') then
|
1036
1053
|
return true
|
1037
1054
|
end
|
1055
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044') then
|
1056
|
+
return true
|
1057
|
+
end
|
1038
1058
|
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0048') then
|
1039
1059
|
return true
|
1040
1060
|
end
|
@@ -1107,6 +1127,9 @@ class GVF1O
|
|
1107
1127
|
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0095') then
|
1108
1128
|
return true
|
1109
1129
|
end
|
1130
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0096') then
|
1131
|
+
return true
|
1132
|
+
end
|
1110
1133
|
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0101') then
|
1111
1134
|
return true
|
1112
1135
|
end
|
@@ -1155,6 +1178,15 @@ class GVF1O
|
|
1155
1178
|
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0154') then
|
1156
1179
|
return true
|
1157
1180
|
end
|
1181
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0156') then
|
1182
|
+
return true
|
1183
|
+
end
|
1184
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0157') then
|
1185
|
+
return true
|
1186
|
+
end
|
1187
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0158') then
|
1188
|
+
return true
|
1189
|
+
end
|
1158
1190
|
return false
|
1159
1191
|
end
|
1160
1192
|
|
@@ -1315,7 +1347,7 @@ class GVF1O
|
|
1315
1347
|
end
|
1316
1348
|
|
1317
1349
|
private
|
1318
|
-
@@parent_properties = { RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0004') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0010') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0012') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0014') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0015') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0021') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0023') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0034') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0036') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0038') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0041') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0042') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0043') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0046') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0047') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0051') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0067') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0053') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0072') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0078') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0079') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0080') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0083') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0090') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0091') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0096') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0102') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0112') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0103') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0112') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0104') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0112') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0119') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0102') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0120') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0103') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0121') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0122') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0123') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0124') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0125') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0126') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0127') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0129') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0128') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0130') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0131') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0147') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0148') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0150') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0152') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0112') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0005') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0007') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0008') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0009') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0013') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0064') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0022') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0024') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0025') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0026') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0027') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0031') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0032') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0037') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0065') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0039') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0048') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0061') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0049') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0061') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0050') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0054') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0055') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0056') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0057') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0073') => 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|
1350
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RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0026') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0027') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0031') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0032') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0037') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0065') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0039') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0158') , 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RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0074') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0076') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0077') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0081') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0082') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0093') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0092') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0094') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0092') , 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RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0156') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0157') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0136') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0088') => RDF::URI.new('http://www.w3.org/2002/07/owl#Thing') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0151') => RDF::URI.new('http://www.w3.org/2002/07/owl#Thing') }
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1352
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end
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