biointerchange 0.1.2 → 0.1.3

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Files changed (30) hide show
  1. data/README.md +49 -4
  2. data/VERSION +1 -1
  3. data/examples/chromosome_BF.gff +1701 -0
  4. data/examples/estd176_Banerjee_et_al_2011.2012-11-29.NCBI36.gvf +4326 -0
  5. data/examples/pubannotation.10096561.json +1 -0
  6. data/examples/{pubannotation.json → pubannotation.10096561.json.old} +0 -0
  7. data/examples/pubannotation.2626671.json +1 -0
  8. data/lib/biointerchange/core.rb +58 -16
  9. data/lib/biointerchange/genomics/gff3_feature.rb +1 -0
  10. data/lib/biointerchange/genomics/gff3_feature_set.rb +31 -1
  11. data/lib/biointerchange/genomics/gff3_pragmas.rb +35 -0
  12. data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +60 -23
  13. data/lib/biointerchange/genomics/gff3_reader.rb +74 -40
  14. data/lib/biointerchange/genomics/gvf_feature.rb +24 -0
  15. data/lib/biointerchange/genomics/gvf_feature_set.rb +14 -0
  16. data/lib/biointerchange/genomics/gvf_pragmas.rb +6 -0
  17. data/lib/biointerchange/genomics/gvf_reader.rb +37 -0
  18. data/lib/biointerchange/gff3o.rb +1 -1
  19. data/lib/biointerchange/gvf1o.rb +145 -17
  20. data/lib/biointerchange/textmining/content.rb +1 -0
  21. data/lib/biointerchange/textmining/content_connection.rb +74 -0
  22. data/lib/biointerchange/textmining/document.rb +3 -1
  23. data/lib/biointerchange/textmining/pubannos_json_reader.rb +87 -9
  24. data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb +58 -2
  25. data/spec/gff3_rdfwriter_spec.rb +9 -1
  26. data/spec/gvf_rdfwriter_spec.rb +81 -0
  27. data/spec/text_mining_pubannos_json_reader_spec.rb +82 -10
  28. data/spec/text_mining_rdfwriter_spec.rb +11 -0
  29. data/web/api.html +30 -23
  30. metadata +156 -138
@@ -0,0 +1,24 @@
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+ module BioInterchange::Genomics
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+
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+ # Represents a single genomic feature of a GVF file.
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+ class GVFFeature < GFF3Feature
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+
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+ # Creates a new feature representation. A feature is described on one line of the GVF file.
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+ #
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+ # +sequence_id+:: an identifier that determines the coordinate system for the feature
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+ # +source+:: a text description of the origin of this feature description
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+ # +type+:: either a SOFA accession, SOFA term, or textual description (the former are URIs, the latter is a string)
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+ # +start_coordinate+:: an integer denoting the start coordinate of the feature
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+ # +end_coordinate+:: an integer denoting the end coordinate of the feature, which is equal or larger than the start coordinate
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+ # +score+:: a floating point score
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+ # +strand+:: a constant determining whether the feature is NOT_STRANDED, the strand is UNKNOWN, or the feature is on the POSITIVE or NEGATIVE strand
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+ # +attributes+:: a map of additional attributes associated with the feature
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+ def initialize(sequence_id, source, type, start_coordinate, end_coordinate, score = nil, strand = NOT_STRANDED, attributes = {})
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+ # Fill in phase, which is always omitted in GVF features (after 'strand', before 'attributes'):
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+ super(sequence_id, source, type, start_coordinate, end_coordinate, score, strand, nil, attributes)
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+ end
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+
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+ end
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+
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+ end
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+
@@ -0,0 +1,14 @@
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+
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+ module BioInterchange::Genomics
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+
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+ # A GVF feature set, which encapsules information of a single GVF file.
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+ class GVFFeatureSet < GFF3FeatureSet
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+
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+ def uri
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+ super.sub(/^biointerchange:\/\/gff3\//, 'biointerchange://gvf/')
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+ end
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+
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+ end
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+
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+ end
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+
@@ -0,0 +1,6 @@
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+
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+ module BioInterchange::Genomics
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+
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+ # TODO
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+
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+ end
@@ -0,0 +1,37 @@
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+ module BioInterchange::Genomics
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+
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+ class GVFReader < GFF3Reader
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+
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+ # Creates a new instance of a Genome Variation Format (GVF) reader.
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+ #
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+ # +name+:: Optional name of the person who generated the GVF file.
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+ # +name_uri+:: Optional e-mail address of the person who generated the GVF file.
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+ # +date+:: Optional date of when the GVF file was produced.
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+ def initialize(name = nil, name_uri = nil, date = nil)
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+ # Remember: calling super without brackets passes all arguments of initialize!
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+ super
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+ end
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+
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+ protected
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+
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+ def create_feature_set
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+ BioInterchange::Genomics::GVFFeatureSet.new()
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+ end
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+
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+ def add_pragma(feature_set, line)
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+ line.chomp!
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+ name, value = line[2..-1].split(/\s/, 2)
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+ value.strip!
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+
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+ # Interpret pragmas, and if not known, delegate to GFF3Reader:
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+ if name == 'gvf-version' then
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+ feature_set.set_pragma(name, { name => value.to_f })
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+ else
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+ super(feature_set, line)
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+ end
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+ end
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+
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+ end
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+
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+ end
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+
@@ -488,7 +488,7 @@ class GFF3O
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  end
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489
 
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  private
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- @@parent_properties = { 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_0025') , 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_0004') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , 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_0032') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0031') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0033') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0031') , 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') }
491
+ @@parent_properties = { 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_0004') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , 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_0032') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0031') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0033') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0031') , 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') }
492
492
 
493
493
  end
494
494
 
@@ -2,10 +2,17 @@ module BioInterchange
2
2
 
3
3
  class GVF1O
4
4
 
5
- # Strand of the feature.
6
- # (http://www.biointerchange.org/gvf1o#GVF1_0010)
5
+ # Either:
6
+ # Strand of the feature.
7
+ # (http://www.biointerchange.org/gvf1o#GVF1_0010)
8
+ # Or:
9
+ # Strand of the breakpoint.
10
+ # (http://www.biointerchange.org/gvf1o#GVF1_0083)
11
+ # Or:
12
+ # Strand of a target -- if applicable.
13
+ # (http://www.biointerchange.org/gvf1o#GVF1_0091)
7
14
  def self.strand
8
- return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0010')
15
+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0010'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0083'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0091') ]
9
16
  end
10
17
 
11
18
  # Tag name/value pair attributes of a feature.
@@ -32,8 +39,11 @@ class GVF1O
32
39
  # Or:
33
40
  # FALDO "Region" instance replacement for a breakpoint's start, stop, strand properties.
34
41
  # (http://www.biointerchange.org/gvf1o#GVF1_0079)
42
+ # Or:
43
+ # FALDO "Region" instance replacement for a target's start, stop, strand properties.
44
+ # (http://www.biointerchange.org/gvf1o#GVF1_0090)
35
45
  def self.region
36
- return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0021'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0079') ]
46
+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0021'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0079'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0090') ]
37
47
  end
38
48
 
39
49
  # NCBI Taxonomy Ontology "NCBITaxon_1" (or sub-classes) instance that denotes the species for a feature set.
@@ -54,6 +64,12 @@ class GVF1O
54
64
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0036')
55
65
  end
56
66
 
67
+ # Zygosity of a variant.
68
+ # (http://www.biointerchange.org/gvf1o#GVF1_0038)
69
+ def self.zygosity
70
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0038')
71
+ end
72
+
57
73
  # An effect of a particular feature variant.
58
74
  # (http://www.biointerchange.org/gvf1o#GVF1_0041)
59
75
  def self.effect
@@ -164,6 +180,22 @@ class GVF1O
164
180
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0078')
165
181
  end
166
182
 
183
+ # Potential source or destination of zero-length sequence alterations.
184
+ # (http://www.biointerchange.org/gvf1o#GVF1_0080)
185
+ def self.breakpoint
186
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0080')
187
+ end
188
+
189
+ # Either:
190
+ # Properties that are directly associated with Target class instances.
191
+ # (http://www.biointerchange.org/gvf1o#GVF1_0089)
192
+ # Or:
193
+ # Properties that are directly associated with Target class instances.
194
+ # (http://www.biointerchange.org/gvf1o#GVF1_0092)
195
+ def self.target_properties
196
+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0092') ]
197
+ end
198
+
167
199
  # Either:
168
200
  # ID of the landmark that establishes the coordinate system for a feature.
169
201
  # (http://www.biointerchange.org/gvf1o#GVF1_0004)
@@ -195,8 +227,11 @@ class GVF1O
195
227
  # Or:
196
228
  # Start coordinate of the feature on the seqid landmark.
197
229
  # (http://www.biointerchange.org/gvf1o#GVF1_0073)
230
+ # Or:
231
+ # Start coordinate of the target.
232
+ # (http://www.biointerchange.org/gvf1o#GVF1_0094)
198
233
  def self.start
199
- return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0007'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0048'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0073') ]
234
+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0007'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0048'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0073'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0094') ]
200
235
  end
201
236
 
202
237
  # Either:
@@ -208,8 +243,11 @@ class GVF1O
208
243
  # Or:
209
244
  # End coordinate of the feature on the seqid landmark.
210
245
  # (http://www.biointerchange.org/gvf1o#GVF1_0074)
246
+ # Or:
247
+ # End coordinate of the target.
248
+ # (http://www.biointerchange.org/gvf1o#GVF1_0095)
211
249
  def self.end
212
- return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0008'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0049'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0074') ]
250
+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0008'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0049'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0074'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0095') ]
213
251
  end
214
252
 
215
253
  # Score of the feature. For example, an E-value for sequence similarity features or a P-value for ab initio gene prediction features.
@@ -226,7 +264,7 @@ class GVF1O
226
264
 
227
265
  # Version of the GVF specification that defines the feature set contents.
228
266
  # (http://www.biointerchange.org/gvf1o#GVF1_0022)
229
- def self.version
267
+ def self.gvf_version
230
268
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0022')
231
269
  end
232
270
 
@@ -284,12 +322,6 @@ class GVF1O
284
322
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0037')
285
323
  end
286
324
 
287
- # Zygosity of a feature locus.
288
- # (http://www.biointerchange.org/gvf1o#GVF1_0038)
289
- def self.zygosity
290
- return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0038')
291
- end
292
-
293
325
  # Frequency of a variant in a population.
294
326
  # (http://www.biointerchange.org/gvf1o#GVF1_0039)
295
327
  def self.variant_freq
@@ -350,6 +382,24 @@ class GVF1O
350
382
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0076')
351
383
  end
352
384
 
385
+ # Version of the GFF specification that defines the feature set contents apart from GVF related definitions.
386
+ # (http://www.biointerchange.org/gvf1o#GVF1_0081)
387
+ def self.gff_version
388
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0081')
389
+ end
390
+
391
+ # Creation date of the GVF file that this set stems from.
392
+ # (http://www.biointerchange.org/gvf1o#GVF1_0082)
393
+ def self.file_date
394
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0082')
395
+ end
396
+
397
+ # ID or accession of the target alignment.
398
+ # (http://www.biointerchange.org/gvf1o#GVF1_0093)
399
+ def self.target_id
400
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0093')
401
+ end
402
+
353
403
  # Set of genomic sequence features, whose identifiers are unique within the set.
354
404
  # (http://www.biointerchange.org/gvf1o#GVF1_0001)
355
405
  def self.Set
@@ -414,6 +464,18 @@ class GVF1O
414
464
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0058')
415
465
  end
416
466
 
467
+ # Denotes the zygosity of alleles.
468
+ # (http://www.biointerchange.org/gvf1o#GVF1_0084)
469
+ def self.Zygosity
470
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0084')
471
+ end
472
+
473
+ # Indicates a feature's "target" of a nucleotide-to-nucleotide or protein-to-nucleotide alignment.
474
+ # (http://www.biointerchange.org/gvf1o#GVF1_0088)
475
+ def self.Target
476
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0088')
477
+ end
478
+
417
479
  # Location on the positive (forward) strand.
418
480
  # (http://www.biointerchange.org/gvf1o#GVF1_0017)
419
481
  def self.Positive
@@ -438,6 +500,24 @@ class GVF1O
438
500
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0020')
439
501
  end
440
502
 
503
+ # Denotes heterozygous alleles.
504
+ # (http://www.biointerchange.org/gvf1o#GVF1_0085)
505
+ def self.Heterozygous
506
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0085')
507
+ end
508
+
509
+ # Denotes homozygous alleles.
510
+ # (http://www.biointerchange.org/gvf1o#GVF1_0086)
511
+ def self.Homozygous
512
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0086')
513
+ end
514
+
515
+ # Denotes hemizygous alleles.
516
+ # (http://www.biointerchange.org/gvf1o#GVF1_0087)
517
+ def self.Hemizygous
518
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0087')
519
+ end
520
+
441
521
  # Determines whether the given URI is an object property.
442
522
  #
443
523
  # +uri+:: URI that is tested for being an object property
@@ -466,6 +546,9 @@ class GVF1O
466
546
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0036') then
467
547
  return true
468
548
  end
549
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0038') then
550
+ return true
551
+ end
469
552
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0041') then
470
553
  return true
471
554
  end
@@ -514,6 +597,21 @@ class GVF1O
514
597
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0079') then
515
598
  return true
516
599
  end
600
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0080') then
601
+ return true
602
+ end
603
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0083') then
604
+ return true
605
+ end
606
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089') then
607
+ return true
608
+ end
609
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0090') then
610
+ return true
611
+ end
612
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0091') then
613
+ return true
614
+ end
517
615
  return false
518
616
  end
519
617
 
@@ -572,9 +670,6 @@ class GVF1O
572
670
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0037') then
573
671
  return true
574
672
  end
575
- if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0038') then
576
- return true
577
- end
578
673
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0039') then
579
674
  return true
580
675
  end
@@ -638,6 +733,24 @@ class GVF1O
638
733
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0077') then
639
734
  return true
640
735
  end
736
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0081') then
737
+ return true
738
+ end
739
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0082') then
740
+ return true
741
+ end
742
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0092') then
743
+ return true
744
+ end
745
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0093') then
746
+ return true
747
+ end
748
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0094') then
749
+ return true
750
+ end
751
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0095') then
752
+ return true
753
+ end
641
754
  return false
642
755
  end
643
756
 
@@ -678,6 +791,12 @@ class GVF1O
678
791
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0058') then
679
792
  return true
680
793
  end
794
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0084') then
795
+ return true
796
+ end
797
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0088') then
798
+ return true
799
+ end
681
800
  return false
682
801
  end
683
802
 
@@ -697,6 +816,15 @@ class GVF1O
697
816
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0020') then
698
817
  return true
699
818
  end
819
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0085') then
820
+ return true
821
+ end
822
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0086') then
823
+ return true
824
+ end
825
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0087') then
826
+ return true
827
+ end
700
828
  return false
701
829
  end
702
830
 
@@ -723,7 +851,7 @@ class GVF1O
723
851
  end
724
852
 
725
853
  private
726
- @@parent_properties = { RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0010') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') , 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_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_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_0004') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , 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_0006') => 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_0029') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0062') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0030') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0062') , 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_0038') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , 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_0060') , 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_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0072') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') , 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') }
854
+ @@parent_properties = { 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_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_0004') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , 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_0006') => 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_0029') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0062') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0030') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0062') , 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_0072') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') , 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_0088') => RDF::URI.new('http://www.w3.org/2002/07/owl#Thing') }
727
855
 
728
856
  end
729
857
 
@@ -63,6 +63,7 @@ class Content
63
63
  "biointerchange://textmining/content/#{@context.uri.sub(/^.*?:\/\//, '')}/#{@offset},#{@length},#{@type},#{process}"
64
64
  end
65
65
 
66
+
66
67
  end
67
68
 
68
69
  end
@@ -0,0 +1,74 @@
1
+ module BioInterchange::TextMining
2
+
3
+ class ContentConnection
4
+
5
+ # Constants that describe content connection type.
6
+ UNSPECIFIED = 0
7
+ EQUIVALENCE = 1
8
+ SUBCLASS = 2
9
+ THEME = 3
10
+ SPECULATION = 4
11
+ NEGATION = 5
12
+
13
+ # Creates a new document content connection representation between specific document content.
14
+ #
15
+ # +content1+:: document content 1
16
+ # +content2+:: document content 2
17
+ # +type+:: classifaction of the connection between the two document content objects
18
+ def initialize(content1, content2, type = UNSPECIFIED, process = nil)
19
+ if content1.nil? and content2.nil?
20
+ raise BioInterchange::Exceptions::ImplementationModelError, 'Content1 and Content2 can not both be nil'
21
+ elsif ( (! content1.kind_of?(BioInterchange::TextMining::Content)) && (! content1.kind_of?(BioInterchange::TextMining::ContentConnection)) && (! content1.nil?) )
22
+ raise BioInterchange::Exceptions::ImplementationModelError, 'Content1 has to be of kind BioInterchange::TextMining::Content or kind BioInterchange::TextMining::ContentConnection'
23
+ elsif ( (! content2.kind_of?(BioInterchange::TextMining::Content)) && (! content2.kind_of?(BioInterchange::TextMining::ContentConnection)) && (! content2.nil?) )
24
+ raise BioInterchange::Exceptions::ImplementationModelError, 'Content2 has to be of kind BioInterchange::TextMining::Content or kind BioInterchange::TextMining::ContentConnection'
25
+ end
26
+ @content1 = content1
27
+ @content2 = content2
28
+ @type = type
29
+ @process = process
30
+ end
31
+
32
+ # Sets the context of this content.
33
+ #
34
+ # +context+:: a +BioInterchange::TextMining::Document+ or +BioInterchange::TextMining::Content+ instance in which this content is enclosed in
35
+ def setContext(context)
36
+ @context = context
37
+ end
38
+
39
+ # Returns the offset of the content as absolute position within the document.
40
+ def content1
41
+ @content1
42
+ end
43
+
44
+ # Returns the length of the content, which is measured in characters.
45
+ def content2
46
+ @content2
47
+ end
48
+
49
+ # Returns the type of the content, if known, or +BioInterchange::TextMining::Content::UNSPECIFIED otherwise.
50
+ def type
51
+ @type
52
+ end
53
+
54
+ # Returns the process associated with this content, if previously provided, or nil otherwise.
55
+ def process
56
+ @process
57
+ end
58
+
59
+ # Returns a URI that identifies this content.
60
+ def uri
61
+ raise BioInterchange::Exceptions::ImplementationModelError, 'An URI can only be returned for content with a context (i.e., use setContext(context) first).' unless @context
62
+ process = '-'
63
+ c1 = '-'
64
+ c2 = '-'
65
+ process = "(#{@process.uri.sub(/^.*?:\/\//, '')})" if @process
66
+ c1 = "#{@content1.uri.sub(/^.*?:\/\//, '')}" if @content1
67
+ c2 = "#{@content2.uri.sub(/^.*?:\/\//, '')}" if @content2
68
+ "biointerchange://textmining/content_connection/#{@context.uri.sub(/^.*?:\/\//, '')}/#{c1},#{c2},#{@type},#{process}"
69
+ end
70
+
71
+ end
72
+
73
+ end
74
+