biointerchange 0.2.0 → 0.2.1

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Files changed (21) hide show
  1. data/README.md +11 -1
  2. data/VERSION +1 -1
  3. data/generators/javaify.rb +1 -1
  4. data/generators/rdfxml.rb +3 -1
  5. data/lib/biointerchange/core.rb +14 -13
  6. data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +61 -9
  7. data/lib/biointerchange/genomics/gff3_reader.rb +5 -1
  8. data/lib/biointerchange/gff3o.rb +44 -28
  9. data/lib/biointerchange/gvf1o.rb +63 -31
  10. data/lib/biointerchange/so.rb +19627 -0
  11. data/spec/gff3_rdfwriter_spec.rb +1 -1
  12. data/spec/gvf_rdfwriter_spec.rb +1 -1
  13. data/supplemental/java/biointerchange/pom.xml +1 -1
  14. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java +97 -63
  15. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java +686 -102
  16. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SO.java +24000 -0
  17. data/supplemental/python/biointerchange/gff3o.py +85 -57
  18. data/supplemental/python/biointerchange/gvf1o.py +565 -84
  19. data/supplemental/python/biointerchange/so.py +19625 -0
  20. data/supplemental/python/setup.py +2 -2
  21. 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
163
163
  </dependency>
164
164
  </dependencies>
165
165
 
166
- Usage examples:
166
+ Current vocabularies:
167
+
168
+ * Generic Feature Format Version 3 Ontology (GFF3O)
169
+ * Genome Variation Format Version 1 Ontology (GVF1O)
170
+
171
+ Usage examples of accessing GFF3O's vocabulary:
167
172
 
168
173
  package org.biointerchange;
169
174
 
@@ -270,6 +275,9 @@ Building a new version of the Ruby vocabulary classes for GFF3, SIO, SOFA (requi
270
275
  echo -e "module BioInterchange\n" > lib/biointerchange/sio.rb
271
276
  ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sio> SIO >> lib/biointerchange/sio.rb
272
277
  echo -e "\nend" >> lib/biointerchange/sio.rb
278
+ echo -e "module BioInterchange\n" > lib/biointerchange/so.rb
279
+ ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-so> SO >> lib/biointerchange/so.rb
280
+ echo -e "\nend" >> lib/biointerchange/so.rb
273
281
  echo -e "module BioInterchange\n" > lib/biointerchange/sofa.rb
274
282
  ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sofa> SOFA >> lib/biointerchange/sofa.rb
275
283
  echo -e "\nend" >> lib/biointerchange/sofa.rb
@@ -287,6 +295,7 @@ The source-code generation can be skipped, if none of the ontologies that are us
287
295
  ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-gff3o> GFF3O | ruby generators/pythonify.rb > supplemental/python/biointerchange/gff3o.py
288
296
  ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-gvf1o> GVF1O | ruby generators/pythonify.rb > supplemental/python/biointerchange/gvf1o.py
289
297
  ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sio> SIO | ruby generators/pythonify.rb > supplemental/python/biointerchange/sio.py
298
+ ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-so> SO | ruby generators/pythonify.rb > supplemental/python/biointerchange/so.py
290
299
  ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sofa> SOFA | ruby generators/pythonify.rb > supplemental/python/biointerchange/sofa.py
291
300
  curl ftp://ftp.geneontology.org/pub/go/doc/GO.xrf_abbs | ruby generators/GOxrefify.rb | ruby generators/pythonify.rb > supplemental/python/biointerchange/goxref.py
292
301
 
@@ -308,6 +317,7 @@ The source-code generation can be skipped, if none of the ontologies that are us
308
317
  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
309
318
  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
310
319
  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
320
+ 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
311
321
  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
312
322
  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
313
323
 
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.2.0
1
+ 0.2.1
data/generators/javaify.rb CHANGED
@@ -51,7 +51,7 @@ STDIN.each { |line|
51
51
  end
52
52
  transduction << " public static #{line.sub('?', '').sub(/self\./, '').sub(/ *def\ /, '')}"
53
53
  method_name = transduction.sub(/^.*public static /m, '').sub(/(\(.*)?$/, '')
54
- transduction.sub!("public static #{method_name}", "public static _#{method_name}_") if method_name.match(/^(true|false|class|public|private|static|return|if|while|do|clone|equals|toString|hashCode)$/)
54
+ 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)$/)
55
55
  variables = transduction.scan(/^\s*public static \w+\((.+)\)$/)
56
56
  variables = variables[0][0].split(',').map { |variable| variable.strip } if variables.length > 0
57
57
  if method_name == 'is_object_property' then
data/generators/rdfxml.rb CHANGED
@@ -80,8 +80,10 @@ model.keys.each { |key|
80
80
  comment = [ uri, " # #{entry[OBO_DEF].to_s.sub(/^"(.*)" \[(.*)\]$/, '\1 (\2)').gsub(/\n|\r\n/, "\n # ")}\n" ]
81
81
  elsif entry[RDF::RDFS.comment] then
82
82
  comment = [ uri, " # #{entry[RDF::RDFS.comment].to_s.gsub(/\n|\r\n/, "\n # ")}\n" ]
83
+ else
84
+ comment = [ uri, " # -- No comment or description provided. --\n" ]
83
85
  end
84
- comments[label_or_synonym] = set | [ comment ] if comment
86
+ comments[label_or_synonym] = set | [ comment ]
85
87
 
86
88
  set = combined_uris[label_or_synonym]
87
89
  set = [] unless set
data/lib/biointerchange/core.rb CHANGED
@@ -24,6 +24,7 @@ module BioInterchange
24
24
  require 'biointerchange/goxref'
25
25
  require 'biointerchange/gvf1o'
26
26
  require 'biointerchange/sio'
27
+ require 'biointerchange/so'
27
28
  require 'biointerchange/sofa'
28
29
 
29
30
  # Reader/writer interfaces
@@ -89,21 +90,21 @@ module BioInterchange
89
90
  begin
90
91
  opt = Getopt::Long.getopts(
91
92
  ["--help", "-h", Getopt::BOOLEAN],
92
- ["--debug", "-d", Getopt::BOOLEAN], # set debug mode => print stack traces
93
+ ["--debug", "-d", Getopt::BOOLEAN], # set debug mode => print stack traces
93
94
  ["--no_rdf_graph_optimization", "-n", Getopt::BOOLEAN], # set self.skip_rdf_graph to false
94
- ["--batchsize", "-b", Getopt::OPTIONAL], # batchsize for readers/writers that support +postpone?+
95
- ["--input", "-i", Getopt::REQUIRED], # input file format
96
- ["--rdf", "-r", Getopt::REQUIRED], # output file format
97
- ["--annotate_name", Getopt::OPTIONAL], # name of resourcce/tool/person
98
- ["--annotate_name_id", Getopt::OPTIONAL], # uri of resource/tool/person
99
- ["--annotate_date", Getopt::OPTIONAL], # date of processing/annotation
100
- ["--annotate_version", Getopt::OPTIONAL], # version number of resource
101
- ["--file", "-f", Getopt::OPTIONAL], # file to read, will read from STDIN if not supplied
102
- ["--out", "-o", Getopt::OPTIONAL], # output file, will out to STDOUT if not supplied
103
- ["--version", "-v", Getopt::OPTIONAL] # output the version number of the gem and exit
95
+ ["--batchsize", "-b", Getopt::OPTIONAL], # batchsize for readers/writers that support +postpone?+
96
+ ["--input", "-i", Getopt::REQUIRED], # input file format
97
+ ["--rdf", "-r", Getopt::REQUIRED], # output file format
98
+ ["--annotate_name", Getopt::OPTIONAL], # name of resourcce/tool/person
99
+ ["--annotate_name_id", Getopt::OPTIONAL], # uri of resource/tool/person
100
+ ["--annotate_date", Getopt::OPTIONAL], # date of processing/annotation
101
+ ["--annotate_version", Getopt::OPTIONAL], # version number of resource
102
+ ["--file", "-f", Getopt::OPTIONAL], # file to read, will read from STDIN if not supplied
103
+ ["--out", "-o", Getopt::OPTIONAL], # output file, will out to STDOUT if not supplied
104
+ ["--version", "-v", Getopt::BOOLEAN] # output the version number of the gem and exit
104
105
  )
105
106
 
106
- if opt['help'] or not opt['input'] or not opt['rdf'] then
107
+ if opt['help'] or not (opt['input'] and opt['rdf'] or opt['version']) then
107
108
  puts "Usage: ruby #{$0} -i <format> -r <format> [options]"
108
109
  puts ''
109
110
  puts 'Supported input formats (--input <format>/-i <format>):'
@@ -154,7 +155,7 @@ module BioInterchange
154
155
 
155
156
  # Print version number and exit:
156
157
  if opt['version'] then
157
- puts 'BioInterchange 0.1.4'
158
+ puts "BioInterchange #{Gem.loaded_specs["biointerchange"].version}"
158
159
  exit
159
160
  end
160
161
 
data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb CHANGED
@@ -145,6 +145,7 @@ protected
145
145
  return if @landmarks.has_key?(landmark.seqid)
146
146
  landmark_uri = RDF::URI.new("#{set_uri.to_s}/landmark/#{landmark.seqid}")
147
147
  @landmarks[landmark.seqid] = landmark_uri
148
+ graph.insert(RDF::Statement.new(landmark_uri, RDF.type, @base.Landmark))
148
149
  graph.insert(RDF::Statement.new(landmark_uri, @base.with_parent([ @base.id ].flatten, @base.landmark_properties)[0], RDF::Literal.new(landmark.seqid)))
149
150
  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
150
151
  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
@@ -164,16 +165,29 @@ protected
164
165
  graph.insert(RDF::Statement.new(feature_uri, @base.alias, RDF::Literal.new(value)))
165
166
  }
166
167
  elsif tag == 'Dbxref' then
167
- feature_properties = @base.feature_properties.select { |uri| @base.is_object_property?(uri) }[0]
168
+ feature_properties = nil
169
+ if @base == BioInterchange::GFF3O then
170
+ feature_properties = @base.feature_properties.select { |uri| @base.is_datatype_property?(uri) }[0]
171
+ else
172
+ feature_properties = @base.feature_properties.select { |uri| @base.is_object_property?(uri) }[0]
173
+ end
168
174
  list.each { |value|
169
175
  begin
176
+ linkout = nil
177
+ # First: determine the Dbxref linkout URI as string
170
178
  if value.match(/^dbSNP(_\d+)?:rs\d+$/) then
171
- graph.insert(RDF::Statement.new(feature_uri, @base.with_parent([ @base.dbxref ].flatten, feature_properties)[0], RDF::URI.new("http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=#{value.split(/:/)[1].sub(/^rs/, '')}")))
179
+ linkout = "http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=#{value.split(/:/)[1].sub(/^rs/, '')}"
172
180
  elsif value.match(/^COSMIC(_\d+)?:COSM\d+$/) then
173
- graph.insert(RDF::Statement.new(feature_uri, @base.with_parent([ @base.dbxref ].flatten, feature_properties)[0], RDF::URI.new("http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=#{value.split(/:/)[1].sub(/^COSM/, '')}")))
181
+ linkout = "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=#{value.split(/:/)[1].sub(/^COSM/, '')}"
174
182
  else
175
183
  abbreviation, id = value.split(':', 2)
176
- graph.insert(RDF::Statement.new(feature_uri, @base.with_parent([ @base.dbxref ].flatten, feature_properties)[0], RDF::URI.new(BioInterchange::GOXRef.send(BioInterchange.make_safe_label(abbreviation)).to_s + id)))
184
+ linkout = BioInterchange::GOXRef.send(BioInterchange.make_safe_label(abbreviation)).to_s + id
185
+ end
186
+ # Second, and finally: add a triple to the graph in the right representative format depending on the ontology used
187
+ if @base == BioInterchange::GFF3O then
188
+ 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
191
  end
178
192
  rescue NoMethodError
179
193
  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
198
212
  list.each { |value|
199
213
  graph.insert(RDF::Statement.new(feature_uri, @base.note, RDF::Literal.new(value)))
200
214
  }
201
- elsif tag == 'Ontology_term' and @base == BioInterchange::GFF3O then
215
+ elsif tag == 'Ontology_term' then
202
216
  list.each { |value|
203
217
  # TODO Sanitize values that are either not in GO xrf_abbs or need conversion to match
204
218
  # match their associated Ruby method.
205
219
  namespace, accession = value.split(/:/, 2)
206
- graph.insert(RDF::Statement.new(feature_uri, @base.ontology_term, RDF::URI.new("#{BioInterchange::GOXRef.send(namespace).to_s}#{accession}")))
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
221
  }
208
222
  elsif tag == 'Parent' then
209
223
  list.each { |parent_id|
@@ -225,6 +239,8 @@ protected
225
239
  graph.insert(RDF::Statement.new(target_uri, @base.with_parent([ @base.end ].flatten, target_object_properties)[0], @base.Positive)) if strand and strand == '+'
226
240
  graph.insert(RDF::Statement.new(target_uri, @base.with_parent([ @base.end ].flatten, target_object_properties)[0], @base.Negative)) if strand and strand == '-'
227
241
  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
244
  elsif tag == 'Variant_seq' and @base == BioInterchange::GVF1O then
229
245
  serialize_variant_seqs(graph, set_uri, feature_uri, list)
230
246
  else
@@ -331,6 +347,28 @@ protected
331
347
  }
332
348
  end
333
349
 
350
+ # Serializes a list of variant effects.
351
+ #
352
+ # +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.insert(RDF::Statement.new(variant_uri, RDF.type, @base.Variant)) unless @variants.has_key?(variant_uri.to_s)
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
data/lib/biointerchange/genomics/gff3_reader.rb CHANGED
@@ -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, 'Type of feature is set to an unknown SOFA term.'
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#GFF3_0006') => 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_0034') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0035') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , 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_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_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') }
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
- # Properties that are directly associated with Effect class instances.
182
- # (http://www.biointerchange.org/gvf1o#GVF1_0070)
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
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') => 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') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0095') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0092') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0101') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0105') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0113') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0106') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0107') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0107') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0113') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0108') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0107') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0132') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0107') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0133') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0107') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0134') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0107') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0137') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0136') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0138') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0136') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0139') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0136') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0149') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0154') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0153') , 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') }
1350
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  end
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