biointerchange 0.1.0 → 0.1.2

data/lib/biointerchange/gvf1o.rb

@@ -0,0 +1,730 @@
+module BioInterchange
+
+class GVF1O
+
+  # Strand of the feature.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0010)
+  def self.strand
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0010')
+  end
+
+  # Tag name/value pair attributes of a feature.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0012)
+  def self.attributes
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0012')
+  end
+
+  # Link out to the parent feature.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0014)
+  def self.parent
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0014')
+  end
+
+  # Relationship that describes which features belong to a feature set.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0015)
+  def self.contains
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0015')
+  end
+
+  # Either:
+  #   FALDO "Region" instance replacement for a feature's start, stop, strand properties.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0021)
+  # Or:
+  #   FALDO "Region" instance replacement for a breakpoint's start, stop, strand properties.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0079)
+  def self.region
+    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0021'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0079') ]
+  end
+
+  # NCBI Taxonomy Ontology "NCBITaxon_1" (or sub-classes) instance that denotes the species for a feature set.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0023)
+  def self.species
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0023')
+  end
+
+  # Specific information about the variant(s) of a feature.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0034)
+  def self.variant
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0034')
+  end
+
+  # Links to information about an individual.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0036)
+  def self.individual
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0036')
+  end
+
+  # An effect of a particular feature variant.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0041)
+  def self.effect
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0041')
+  end
+
+  # Effect of a sequence alteration on a sequence feature.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0042)
+  def self.sequence_variant
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0042')
+  end
+
+  # A term that is describing the sequence feature that is being affected.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0043)
+  def self.feature_type
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0043')
+  end
+
+  # Features that are affected by this sequence alteration effect.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0044)
+  def self.feature_id
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044')
+  end
+
+  # A coordinate range for ambiguous start coordinates.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0046)
+  def self.start_range
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0046')
+  end
+
+  # A coordinate range for ambiguous start coordinates.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0047)
+  def self.end_range
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0047')
+  end
+
+  # Denotes abstract chromosome representations for capturing variants that appear on the same chromosome of a polyploid organism.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0051)
+  def self.chromosome
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0051')
+  end
+
+  # Determines the genotype as observed in an individual.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0053)
+  def self.genotype
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0053')
+  end
+
+  # Either:
+  #   Properties that are directly associated with Feature class instances.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0066)
+  # Or:
+  #   Properties that are directly associated with Feature class instances.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0059)
+  def self.feature_properties
+    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') ]
+  end
+
+  # Either:
+  #   Properties that are directly associated with SequencedIndividual class instances.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0067)
+  # Or:
+  #   Properties that are directly associated with SequencedIndividual class instances.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0065)
+  def self.sequencedindividual_properties
+    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0067'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0065') ]
+  end
+
+  # Either:
+  #   Properties that are directly associated with Set class instances.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0068)
+  # Or:
+  #   Properties that are directly associated with Set class instances.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0063)
+  def self.set_properties
+    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') ]
+  end
+
+  # Either:
+  #   Properties that are directly associated with Variant class instances.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0069)
+  # Or:
+  #   Properties that are directly associated with Variant class instances.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0060)
+  def self.variant_properties
+    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') ]
+  end
+
+  # Properties that are directly associated with Effect class instances.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0070)
+  def self.effect_properties
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070')
+  end
+
+  # Either:
+  #   Properties that are directly associated with Breakpoint class instances.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0075)
+  # Or:
+  #   Properties that are directly associated with Breakpoint class instances.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0071)
+  def self.breakpoint_properties
+    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') ]
+  end
+
+  # A database cross-reference to associate a sequence alteration to its  representation in another database.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0078)
+  def self.dbxref
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0078')
+  end
+
+  # Either:
+  #   ID of the landmark that establishes the coordinate system for a feature.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0004)
+  # Or:
+  #   ID of the landmark that establishes the coordinate system for a breakpoint.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0072)
+  def self.seqid
+    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0004'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0072') ]
+  end
+
+  # 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.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0005)
+  def self.source
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0005')
+  end
+
+  # Type of the feature, which is either a term from the "lite" version of the Sequence Ontology (SOFA), a term from the full Sequence Ontology (SO) that is a child of sequence_feature (SO:0000110), or a SOFA or SO accession number.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0006)
+  def self.type
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006')
+  end
+
+  # Either:
+  #   Start coordinate of the feature on the seqid landmark.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0007)
+  # Or:
+  #   A coordinate that defines the start of an ambiguous coordinate range.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0048)
+  # Or:
+  #   Start coordinate of the feature on the seqid landmark.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0073)
+  def self.start
+    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') ]
+  end
+
+  # Either:
+  #   End coordinate of the feature on the seqid landmark.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0008)
+  # Or:
+  #   A coordinate that defines the end of an ambiguous coordinate range.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0049)
+  # Or:
+  #   End coordinate of the feature on the seqid landmark.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0074)
+  def self.end
+    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') ]
+  end
+
+  # Score of the feature. For example, an E-value for sequence similarity features or a P-value for ab initio gene prediction features.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0009)
+  def self.score
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0009')
+  end
+
+  # Tag name of a feature attribute.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0013)
+  def self.tag
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0013')
+  end
+
+  # Version of the GVF specification that defines the feature set contents.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0022)
+  def self.version
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0022')
+  end
+
+  # Name of a genome assembly build that denotes the provenance of features in a feature set. For example, 'NCBI 36' or 'FlyBase r4.1'.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0024)
+  def self.build
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0024')
+  end
+
+  # All sequence variations at a locus -- including the reference sequence when appropriate (for example, when the locus is heterozygous). If the feature is on the minus strand, then the sequence is the reverse-compliment of the reference genome for these coordinates.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0025)
+  def self.variant_seq
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0025')
+  end
+
+  # A unique identifier for the feature within the feature set.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0026)
+  def self.id
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0026')
+  end
+
+  # Secondary name of a feature, which can be HGVS/ISCN nomenclature names, but not cross-references to databases (e.g. dbSNP, OMIM) which should use the dbxref property.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0027)
+  def self.alias
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0027')
+  end
+
+  # Name of an external database. For example, "dbSNP" or "OMIM".
+  # (http://www.biointerchange.org/gvf1o#GVF1_0029)
+  def self.name
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0029')
+  end
+
+  # External database identifier. For example, for dbSNP, this identifier could be "rs3131969".
+  # (http://www.biointerchange.org/gvf1o#GVF1_0030)
+  def self.xref
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0030')
+  end
+
+  # Sequence from the reference genome.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0031)
+  def self.reference_seq
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0031')
+  end
+
+  # Number of reads that are supporting this variant.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0032)
+  def self.variant_reads
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0032')
+  end
+
+  # Total number of reads.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0037)
+  def self.total_reads
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0037')
+  end
+
+  # Zygosity of a feature locus.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0038)
+  def self.zygosity
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0038')
+  end
+
+  # Frequency of a variant in a population.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0039)
+  def self.variant_freq
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0039')
+  end
+
+  # Unclear from GVF specification.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0050)
+  def self.phased
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0050')
+  end
+
+  # Describes the codon that overlaps this variant.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0054)
+  def self.variant_codon
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0054')
+  end
+
+  # Describes the codon from the reference sequence whose coordinates overlap with this variant.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0055)
+  def self.reference_codon
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0055')
+  end
+
+  # Amino acid that overlaps with the variant.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0056)
+  def self.variant_aa
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0056')
+  end
+
+  # Amino acid in the reference genome that overlaps with a variant's genome coordinates.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0057)
+  def self.reference_aa
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0057')
+  end
+
+  # Properties that are directly associated with Range class instances.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0061)
+  def self.range_properties
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0061')
+  end
+
+  # Properties that are directly associated with DBXRef class instances.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0062)
+  def self.dbxref_properties
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0062')
+  end
+
+  # Properties that are directly associated with Attribute class instances.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0064)
+  def self.attribute_properties
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0064')
+  end
+
+  # Sequence context (positive strand) of a feature on the 5' end.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0076)
+  def self.a_context
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0076')
+  end
+
+  # Set of genomic sequence features, whose identifiers are unique within the set.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0001)
+  def self.Set
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0001')
+  end
+
+  # A genomic sequence feature.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0002)
+  def self.Feature
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0002')
+  end
+
+  def self.Attribute
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0003')
+  end
+
+  # Class describing a genomic strand. Instances of the class (individuals) are used to denote forward-/reverse-strands, etc.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0016)
+  def self.Strand
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0016')
+  end
+
+  # A class describing relationships between features and external databases.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0028)
+  def self.DBXRef
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0028')
+  end
+
+  # Describing specific alterations of a feature.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0033)
+  def self.Variant
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0033')
+  end
+
+  # Aggregated sequencing information for a particular individual.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0035)
+  def self.SequencedIndividual
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0035')
+  end
+
+  # Describing the effect of a feature variant.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0040)
+  def self.Effect
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0040')
+  end
+
+  # Describe ambiguity in either start or end coordinates.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0045)
+  def self.Range
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0045')
+  end
+
+  # An abstract representation of a chromosome to represent ploidy.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0052)
+  def self.Chromosome
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0052')
+  end
+
+  # Describes the source or destination of a zero-length sequence alteration.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0058)
+  def self.Breakpoint
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0058')
+  end
+
+  # Location on the positive (forward) strand.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0017)
+  def self.Positive
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0017')
+  end
+
+  # Location on the negative (reverse) strand.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0018)
+  def self.Negative
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0018')
+  end
+
+  # Strand was not determined, which leaves it open whether the location is on the positive (forward) or negative (reverse) strand.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0019)
+  def self.UnknownStrand
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0019')
+  end
+
+  # Strand is not applicable.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0020)
+  def self.NotStranded
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0020')
+  end
+
+  # Determines whether the given URI is an object property.
+  #
+  # +uri+:: URI that is tested for being an object property
+  def self.is_object_property?(uri)
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0010') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0012') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0014') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0015') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0021') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0023') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0034') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0036') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0041') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0042') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0043') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0046') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0047') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0051') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0053') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0067') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0078') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0079') then
+      return true
+    end
+    return false
+  end
+
+  # Determines whether the given URI is a datatype property.
+  #
+  # +uri+:: URI that is tested for being a datatype property
+  def self.is_datatype_property?(uri)
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0004') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0005') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0007') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0008') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0009') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0013') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0022') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0024') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0025') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0026') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0027') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0029') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0030') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0031') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0032') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0037') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0038') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0039') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0048') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0049') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0050') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0054') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0055') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0056') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0057') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0061') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0062') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0064') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0065') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0072') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0073') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0074') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0076') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0077') then
+      return true
+    end
+    return false
+  end
+
+  # Determines whether the given URI is a class.
+  #
+  # +uri+:: URI that is tested for being a class
+  def self.is_class?(uri)
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0001') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0002') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0003') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0016') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0028') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0033') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0035') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0040') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0045') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0052') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0058') then
+      return true
+    end
+    return false
+  end
+
+  # Determines whether the given URI is a named individual.
+  #
+  # +uri+:: URI that is tested for being a named individual
+  def self.is_named_individual?(uri)
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0017') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0018') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0019') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0020') then
+      return true
+    end
+    return false
+  end
+
+  # Returns only those URIs that fall under a designated parent URI.
+  #
+  # +uris+:: Set of URIs that are tested whether they have the given parent URI.
+  # +parent+:: Parent URI.
+  def self.with_parent(uris, parent)
+    return uris.select { |uri| has_parent?(uri, parent) }
+  end
+
+  # Recursively tries to determine the parent for a given URI.
+  #
+  # +uri+:: URI that is tested for whether it has the given parent URI.
+  # +parent+:: Parent URI.
+  def self.has_parent?(uri, parent)
+    if @@parent_properties.has_key?(uri) then
+      if @@parent_properties[uri] == parent then
+        return true
+      end
+      return has_parent?(@@parent_properties[uri], parent)
+    end
+    return false
+  end
+
+private
+  @@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') }
+
+end
+
+end