class BioInterchange::GFVO

Public Class Methods

Alias() click to toggle source

An alias is an alternative name whose use is mostly non-primary. (www.biointerchange.org/gfvo#Alias)

# File lib/biointerchange/gfvo.rb, line 208
def self.Alias
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Alias')
end
AlleleFrequency() click to toggle source

Proportion of a particular gene allele in a gene pool. (www.biointerchange.org/gfvo#AlleleFrequency)

# File lib/biointerchange/gfvo.rb, line 214
def self.AlleleFrequency
  return RDF::URI.new('http://www.biointerchange.org/gfvo#AlleleFrequency')
end
AminoAcid() click to toggle source

– No comment or description provided. – (www.biointerchange.org/gfvo#AminoAcid)

# File lib/biointerchange/gfvo.rb, line 220
def self.AminoAcid
  return RDF::URI.new('http://www.biointerchange.org/gfvo#AminoAcid')
end
AncestralSequence() click to toggle source

Denotes an ancestral allele of a feature. May be used to denote the ‘ancestral allele’ of VCF formatted files. (www.biointerchange.org/gfvo#AncestralSequence)

# File lib/biointerchange/gfvo.rb, line 226
def self.AncestralSequence
  return RDF::URI.new('http://www.biointerchange.org/gfvo#AncestralSequence')
end
ArrayComparativeGenomicHybridization() click to toggle source

Feature provenance is based on array-comparative genomic hybridization. (www.biointerchange.org/gfvo#ArrayComparativeGenomicHybridization)

# File lib/biointerchange/gfvo.rb, line 232
def self.ArrayComparativeGenomicHybridization
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ArrayComparativeGenomicHybridization')
end
Attribute() click to toggle source

An attribute denotes characteristics of an entity. At this stage, “Quality” is the only direct subclass of “Attribute”, whose subclasses denote qualitative properties such as sex (“Female”, “Male”, “Mermaphrodite”), zygosity (“Hemizygous”, “Heterozygous”, “Homozygous”), etc.

The object property “hasQuality” (or subproperties thereof) should be utilized to express qualities of entities. The “hasAttribute” object property should be used to denote relationships to “Object” or “Process” instances, unless there is a better object property suitable to represent the relationship between the involved entities.. (www.biointerchange.org/gfvo#Attribute)

# File lib/biointerchange/gfvo.rb, line 240
def self.Attribute
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Attribute')
end
AverageCoverage() click to toggle source

Average coverage depth for a genomic locus (a region or single base pair), i.e. the average number of reads representing a given nucleotide in the reconstructed sequence. (www.biointerchange.org/gfvo#AverageCoverage)

# File lib/biointerchange/gfvo.rb, line 246
def self.AverageCoverage
  return RDF::URI.new('http://www.biointerchange.org/gfvo#AverageCoverage')
end
BiologicalEntity() click to toggle source

A biological entity an entity that contains genomic material or utilizes genomic material during its existance. Genomic material itself is represented as sub-classes of Chemical Entity. (www.biointerchange.org/gfvo#BiologicalEntity)

# File lib/biointerchange/gfvo.rb, line 252
def self.BiologicalEntity
  return RDF::URI.new('http://www.biointerchange.org/gfvo#BiologicalEntity')
end
BiopolymerSequencing() click to toggle source

Information about features and variants is based on biopolymer sequencing. (www.biointerchange.org/gfvo#BiopolymerSequencing)

# File lib/biointerchange/gfvo.rb, line 258
def self.BiopolymerSequencing
  return RDF::URI.new('http://www.biointerchange.org/gfvo#BiopolymerSequencing')
end
Breakpoint() click to toggle source

A breakpoint describes the source or destination of a zero-length sequence alteration. These alterations are typically insertions, deletions or translocations according to the GVF specification (see “Breakpoint_detail” in sequenceontology.org/resources/gvf.html). (www.biointerchange.org/gfvo#Breakpoint)

# File lib/biointerchange/gfvo.rb, line 264
def self.Breakpoint
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Breakpoint')
end
Catalog() click to toggle source

A catalog is a specialization of a “Collection”, where all its contents are of the same type. (www.biointerchange.org/gfvo#Catalog)

# File lib/biointerchange/gfvo.rb, line 270
def self.Catalog
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Catalog')
end
Cell() click to toggle source

A cell is a biological unit that in itself forms a living organism or is part of a larger organism that is composed of many other cells. (www.biointerchange.org/gfvo#Cell)

# File lib/biointerchange/gfvo.rb, line 276
def self.Cell
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Cell')
end
ChemicalEntity() click to toggle source

A chemical entity is an entity related to chemistry. This class is typically not instantiated, but instead, its subclasses “Amino Acid”, “Chromosome”, “Peptide Sequence”, etc., are used to represent specific chemical entities. (www.biointerchange.org/gfvo#ChemicalEntity)

# File lib/biointerchange/gfvo.rb, line 282
def self.ChemicalEntity
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ChemicalEntity')
end
Chromosome() click to toggle source

A chromosome is an abstract representation of an unnamed chromosome to represent ploidy within a data set. A “Chromosome” instance is used for for denoting the locus of phased genotypes. For placing genomic features (“Feature” class instances) on a chromosome, contig, scaffold, etc., please see the “Landmark” class. (www.biointerchange.org/gfvo#Chromosome)

# File lib/biointerchange/gfvo.rb, line 288
def self.Chromosome
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Chromosome')
end
CircularHelix() click to toggle source

A circular helix structure.

Can be used to indicate a true “Is_circular” attribute in GFF3 and GVF. (www.biointerchange.org/gfvo#CircularHelix)

# File lib/biointerchange/gfvo.rb, line 296
def self.CircularHelix
  return RDF::URI.new('http://www.biointerchange.org/gfvo#CircularHelix')
end
CodingFrameOffset() click to toggle source

Coding frame offset of the feature, if it is a coding sequence or feature that contributes to transcription and translation. It is referred to as “frame” in GTF, but called “phase” in GFF3 and GVF. A feature’s coding frame offset can be either 0, 1, or 2. (www.biointerchange.org/gfvo#CodingFrameOffset)

# File lib/biointerchange/gfvo.rb, line 302
def self.CodingFrameOffset
  return RDF::URI.new('http://www.biointerchange.org/gfvo#CodingFrameOffset')
end
CodonSequence() click to toggle source

A codon sequence is a nucleotide sequence underlying a potential amino acid sequence. Codon sequences are three bases of length or multiples thereof. (www.biointerchange.org/gfvo#CodonSequence)

# File lib/biointerchange/gfvo.rb, line 308
def self.CodonSequence
  return RDF::URI.new('http://www.biointerchange.org/gfvo#CodonSequence')
end
Collection() click to toggle source

A collection is a container for genomic data. A collection may contain information about genomic data including – but not limited to – contents of GFF3, GTF, GVF and VCF files. The latter are better represented by “File” class instances, whereas the result of unions or intersections between different “File” class instances should be captured within this format-independent “Collection” class. When importing data whose provenance is not a GFF3, GTF, GVF or VCF file, instances of “Collection” should be utilized too, or the more restrictive “Catalog” class should be used. (www.biointerchange.org/gfvo#Collection)

# File lib/biointerchange/gfvo.rb, line 314
def self.Collection
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Collection')
end
Comment() click to toggle source

A comment is a remark about a piece of information, an observation or statement. In the context of GFF3, GVF, etc., genomic feature and variation descriptions, “isAfter” and “isBefore” relationships should be used to indicate where a comment is situated between pragma or feature statements of GFF3, GTF, GVF or VCF files. (www.biointerchange.org/gfvo#Comment)

# File lib/biointerchange/gfvo.rb, line 320
def self.Comment
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Comment')
end
Contig() click to toggle source

A contig is a contiguous DNA sequence that has been assembled from shorter overlapping DNA segments. (www.biointerchange.org/gfvo#Contig)

# File lib/biointerchange/gfvo.rb, line 326
def self.Contig
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Contig')
end
Coverage() click to toggle source

Number of nucleic acid sequence reads for a particular genomic locus (a region or single base pair). (www.biointerchange.org/gfvo#Coverage)

# File lib/biointerchange/gfvo.rb, line 332
def self.Coverage
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Coverage')
end
DNAMicroarray() click to toggle source

Feature information is based on DNA microarray probes. (www.biointerchange.org/gfvo#DNAMicroarray)

# File lib/biointerchange/gfvo.rb, line 338
def self.DNAMicroarray
  return RDF::URI.new('http://www.biointerchange.org/gfvo#DNAMicroarray')
end
DNASequence() click to toggle source

– No comment or description provided. – (www.biointerchange.org/gfvo#DNASequence)

# File lib/biointerchange/gfvo.rb, line 344
def self.DNASequence
  return RDF::URI.new('http://www.biointerchange.org/gfvo#DNASequence')
end
DNASequencing() click to toggle source

Information about features and variants is based on DNA sequencing. (www.biointerchange.org/gfvo#DNASequencing)

# File lib/biointerchange/gfvo.rb, line 350
def self.DNASequencing
  return RDF::URI.new('http://www.biointerchange.org/gfvo#DNASequencing')
end
ExperimentalMethod() click to toggle source

An experimental method is a procedure that yields an experimental outcome (result). Experimental methods can be in vivo, in vitro or in silico procedures that are well described and can be referenced. (www.biointerchange.org/gfvo#ExperimentalMethod)

# File lib/biointerchange/gfvo.rb, line 356
def self.ExperimentalMethod
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ExperimentalMethod')
end
ExternalReference() click to toggle source

A cross-reference to associate an entity to a representation in another database. (www.biointerchange.org/gfvo#ExternalReference)

# File lib/biointerchange/gfvo.rb, line 362
def self.ExternalReference
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ExternalReference')
end
Feature() click to toggle source

The feature class captures information about genomic sequence features and variations. A genomic feature can be a large object, such as a chromosome or contig, down to single base-pair reference or variant alleles. (www.biointerchange.org/gfvo#Feature)

# File lib/biointerchange/gfvo.rb, line 368
def self.Feature
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Feature')
end
Female() click to toggle source

Denoting sex of a female individual. A female is defined as an individual producing ova. (www.biointerchange.org/gfvo#Female)

# File lib/biointerchange/gfvo.rb, line 374
def self.Female
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Female')
end
File() click to toggle source

A file represents the contents of a GFF3, GTF, GVF or VCF file. It can capture genomic meta-data that is specific to any of these file formats. The result of unions, intersections or other operations between “File” class instances should be capture with the generic “Collection” class, which is format independent, or the more restrictive “Catalog” class should be used. (www.biointerchange.org/gfvo#File)

# File lib/biointerchange/gfvo.rb, line 380
def self.File
  return RDF::URI.new('http://www.biointerchange.org/gfvo#File')
end
ForwardReferenceSequenceFrameshift() click to toggle source

Denotes a frameshift forward in the reference sequence. (www.biointerchange.org/gfvo#ForwardReferenceSequenceFrameshift)

# File lib/biointerchange/gfvo.rb, line 386
def self.ForwardReferenceSequenceFrameshift
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ForwardReferenceSequenceFrameshift')
end
FragmentReadPlatform() click to toggle source

Details about the fragment-read (single-end read) sequencing technology used to gather the data in a set. (www.biointerchange.org/gfvo#FragmentReadPlatform)

# File lib/biointerchange/gfvo.rb, line 392
def self.FragmentReadPlatform
  return RDF::URI.new('http://www.biointerchange.org/gfvo#FragmentReadPlatform')
end
FunctionalSpecification() click to toggle source

A functional specification of bioinformatics data, i.e. the specification of genomic material that potentially has biological function. (www.biointerchange.org/gfvo#FunctionalSpecification)

# File lib/biointerchange/gfvo.rb, line 398
def self.FunctionalSpecification
  return RDF::URI.new('http://www.biointerchange.org/gfvo#FunctionalSpecification')
end
GameticPhase() click to toggle source

Denotes the presence of information that required capturing the gametic phase. For diploid organisms, that means that information is available about which chromosome of a chromosome pair contributed data. (www.biointerchange.org/gfvo#GameticPhase)

# File lib/biointerchange/gfvo.rb, line 404
def self.GameticPhase
  return RDF::URI.new('http://www.biointerchange.org/gfvo#GameticPhase')
end
Genome() click to toggle source

Representation of a genome. Genomic features that constitute the genome may be linked via one or more “Collection”, “Catalog”, “Contig”, “Scaffold” or “File” instances. (www.biointerchange.org/gfvo#Genome)

# File lib/biointerchange/gfvo.rb, line 410
def self.Genome
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Genome')
end
GenomeAnalysis() click to toggle source

A genome analysis denotes the type of procedure that was carried out to derive information from a genome assembly. (www.biointerchange.org/gfvo#GenomeAnalysis)

# File lib/biointerchange/gfvo.rb, line 416
def self.GenomeAnalysis
  return RDF::URI.new('http://www.biointerchange.org/gfvo#GenomeAnalysis')
end
GenomicAscertainingMethod() click to toggle source

Provides information about the source of the data. (www.biointerchange.org/gfvo#GenomicAscertainingMethod)

# File lib/biointerchange/gfvo.rb, line 422
def self.GenomicAscertainingMethod
  return RDF::URI.new('http://www.biointerchange.org/gfvo#GenomicAscertainingMethod')
end
Genotype() click to toggle source

The genotype is the genetic information captured in a particular genome. It can also refer to one or more populations, if statistical distributions are provided that assign genetic codes to groups of individuals.

A genotype is denoted by a string of slash-separated list of alleles (“has value” property). The length of the list is dependent on the ploidy of the studied species as well as sequencing technique used.

Example: “A/G” denotes a genotype with alleles “A” and “G”. (www.biointerchange.org/gfvo#Genotype)

# File lib/biointerchange/gfvo.rb, line 432
def self.Genotype
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Genotype')
end
Genotyping() click to toggle source

Genotyping is the process of determining the genetics of an individual or sample. The genotype itself is expressed as the difference of genetic mark-up compared to a reference genome. (www.biointerchange.org/gfvo#Genotyping)

# File lib/biointerchange/gfvo.rb, line 438
def self.Genotyping
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Genotyping')
end
GermlineCell() click to toggle source

The germline feature class captures information about genomic sequence features arising from germline cells. (www.biointerchange.org/gfvo#GermlineCell)

# File lib/biointerchange/gfvo.rb, line 444
def self.GermlineCell
  return RDF::URI.new('http://www.biointerchange.org/gfvo#GermlineCell')
end
HelixStructure() click to toggle source

Helix structure denotes the physical shape of biopolymers. (www.biointerchange.org/gfvo#HelixStructure)

# File lib/biointerchange/gfvo.rb, line 450
def self.HelixStructure
  return RDF::URI.new('http://www.biointerchange.org/gfvo#HelixStructure')
end
Hemizygous() click to toggle source

A sequence alteration with hemizygous alleles. (www.biointerchange.org/gfvo#Hemizygous)

# File lib/biointerchange/gfvo.rb, line 456
def self.Hemizygous
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Hemizygous')
end
Heritage() click to toggle source

Heritage denotes the passing of traits from parents or ancestors. Passed traits may not be visible as a phenotype, but instead, might only manifest as genetic inheritance. (www.biointerchange.org/gfvo#Heritage)

# File lib/biointerchange/gfvo.rb, line 462
def self.Heritage
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Heritage')
end
Hermaphrodite() click to toggle source

Denoting sex of an individual that contains both male and female gametes. (www.biointerchange.org/gfvo#Hermaphrodite)

# File lib/biointerchange/gfvo.rb, line 468
def self.Hermaphrodite
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Hermaphrodite')
end
Heterozygous() click to toggle source

A sequence alteration with heterozygous alleles. (www.biointerchange.org/gfvo#Heterozygous)

# File lib/biointerchange/gfvo.rb, line 474
def self.Heterozygous
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Heterozygous')
end
Homozygous() click to toggle source

A sequence alteration with homozygous alleles. (www.biointerchange.org/gfvo#Homozygous)

# File lib/biointerchange/gfvo.rb, line 480
def self.Homozygous
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Homozygous')
end
Identifier() click to toggle source

An identifier labels an entity with a single term that is interpreted as an accession. An accession labels entities that are part of a collection of similar type. (www.biointerchange.org/gfvo#Identifier)

# File lib/biointerchange/gfvo.rb, line 486
def self.Identifier
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Identifier')
end
InformationContentEntity() click to toggle source

An information content entity requires background information or specific domain knowledge to be interpreted correctly. (www.biointerchange.org/gfvo#InformationContentEntity)

# File lib/biointerchange/gfvo.rb, line 492
def self.InformationContentEntity
  return RDF::URI.new('http://www.biointerchange.org/gfvo#InformationContentEntity')
end
Interaction() click to toggle source

Describing interaction between features, such as the effect of a feature variant on another feature. (www.biointerchange.org/gfvo#Interaction)

# File lib/biointerchange/gfvo.rb, line 498
def self.Interaction
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Interaction')
end
Label() click to toggle source

A label is a term or short list of terms that name an entity for the purpose of lexicographically distinguishing the entity from entities of similar type. (www.biointerchange.org/gfvo#Label)

# File lib/biointerchange/gfvo.rb, line 504
def self.Label
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Label')
end
Landmark() click to toggle source

A landmark establishes a coordinate system for features. Landmarks can be chromosomes, contigs, scaffolds or other constructs that can harbor “Feature” class instances. For expressing ploidy within a data set, please refer to the “Chromosome” class. (www.biointerchange.org/gfvo#Landmark)

# File lib/biointerchange/gfvo.rb, line 510
def self.Landmark
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Landmark')
end
Likelihood() click to toggle source

Likelihood is the hypothetical probability of the occurrence of a certain event. (www.biointerchange.org/gfvo#Likelihood)

# File lib/biointerchange/gfvo.rb, line 516
def self.Likelihood
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Likelihood')
end
Locus() click to toggle source

A locus refers to a position (possibly multi-dimensional) within a genome or proteome. (www.biointerchange.org/gfvo#Locus)

# File lib/biointerchange/gfvo.rb, line 522
def self.Locus
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Locus')
end
Male() click to toggle source

Denoting sex of a male individual. A male is defined as an individual producing spermatozoa. (www.biointerchange.org/gfvo#Male)

# File lib/biointerchange/gfvo.rb, line 528
def self.Male
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Male')
end
Match() click to toggle source

Denotes a match between the reference sequence and target sequence. (www.biointerchange.org/gfvo#Match)

# File lib/biointerchange/gfvo.rb, line 534
def self.Match
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Match')
end
MaterialEntity() click to toggle source

A material entity represents a physical object. In the context of genomic features and variations, material entities are cells, organisms, sequences, chromosomes, etc. (www.biointerchange.org/gfvo#MaterialEntity)

# File lib/biointerchange/gfvo.rb, line 540
def self.MaterialEntity
  return RDF::URI.new('http://www.biointerchange.org/gfvo#MaterialEntity')
end
MaternalHeritage() click to toggle source

Maternal heritage is the passing of traits from a female to her ancestors. (www.biointerchange.org/gfvo#MaternalHeritage)

# File lib/biointerchange/gfvo.rb, line 546
def self.MaternalHeritage
  return RDF::URI.new('http://www.biointerchange.org/gfvo#MaternalHeritage')
end
MobileElementSequenceVariant() click to toggle source

Insertion or deletion of a mobile element. The exact modification is determined by a type of the Variation Ontology. (www.biointerchange.org/gfvo#MobileElementSequenceVariant)

# File lib/biointerchange/gfvo.rb, line 552
def self.MobileElementSequenceVariant
  return RDF::URI.new('http://www.biointerchange.org/gfvo#MobileElementSequenceVariant')
end
Name() click to toggle source

A name assigns an entity a non-formal term (or multiples thereof) that can provide information about the entities identity. (www.biointerchange.org/gfvo#Name)

# File lib/biointerchange/gfvo.rb, line 558
def self.Name
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Name')
end
Note() click to toggle source

A note is a short textual description. (www.biointerchange.org/gfvo#Note)

# File lib/biointerchange/gfvo.rb, line 564
def self.Note
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Note')
end
Number_ofReads() click to toggle source

Number of reads supporting a particular feature or variant. (www.biointerchange.org/gfvo#NumberOfReads)

# File lib/biointerchange/gfvo.rb, line 570
def self.Number_ofReads
  return RDF::URI.new('http://www.biointerchange.org/gfvo#NumberOfReads')
end
Object() click to toggle source

An object is a concrete entity that realizes a concept and encapsulates data associated with said concept. Objects are typically representing tangible entities, such as “Chromosome”, “DNA Sequence”, but also objects such as “Identifier”, “Average Coverage” or other computational or mathematical entities. (www.biointerchange.org/gfvo#Object)

# File lib/biointerchange/gfvo.rb, line 576
def self.Object
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Object')
end
PairedEndReadPlatform() click to toggle source

Details about the paired-end read sequencing technology used to gather the data in a set. (www.biointerchange.org/gfvo#PairedEndReadPlatform)

# File lib/biointerchange/gfvo.rb, line 582
def self.PairedEndReadPlatform
  return RDF::URI.new('http://www.biointerchange.org/gfvo#PairedEndReadPlatform')
end
PaternalHeritage() click to toggle source

Paternal heritage is the passing of traits from a male to his ancestors. (www.biointerchange.org/gfvo#PaternalHeritage)

# File lib/biointerchange/gfvo.rb, line 588
def self.PaternalHeritage
  return RDF::URI.new('http://www.biointerchange.org/gfvo#PaternalHeritage')
end
PeptideSequence() click to toggle source

A peptide sequence is an ordered sequence of amino acid residues, but which may not necessarily be a protein sequence. For encoding sequences of proteins, the subclass “Protein Sequence” should be used. (www.biointerchange.org/gfvo#PeptideSequence)

# File lib/biointerchange/gfvo.rb, line 594
def self.PeptideSequence
  return RDF::URI.new('http://www.biointerchange.org/gfvo#PeptideSequence')
end
Phenotype() click to toggle source

A phenotype description represents additional information about a sequenced individual’s phenotype. A sequenced individual is represented by instances of the “Sequenced Individual” class. (www.biointerchange.org/gfvo#Phenotype)

# File lib/biointerchange/gfvo.rb, line 600
def self.Phenotype
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Phenotype')
end
PhredScore() click to toggle source

The Phred score can be used to assign quality scores to base calls of DNA sequences. (www.biointerchange.org/gfvo#PhredScore)

# File lib/biointerchange/gfvo.rb, line 606
def self.PhredScore
  return RDF::URI.new('http://www.biointerchange.org/gfvo#PhredScore')
end
PrenatalCell() click to toggle source

A prenatal feature is purportedly associated with prenatal cells; the GVF specification declares this feature type under the prama directive “##genomic-source”, but does not describe its semantics and the referenced Logical Observation Identifiers Names and Codes (LOINC, loinc.org), do not define the meaning or intended usage of the term “prenatal” either. (www.biointerchange.org/gfvo#PrenatalCell)

# File lib/biointerchange/gfvo.rb, line 612
def self.PrenatalCell
  return RDF::URI.new('http://www.biointerchange.org/gfvo#PrenatalCell')
end
Process() click to toggle source

A process denotes a temporally dependent entity. It can be thought of as a function, where input data is transformed by an algorithm to produce certain output data. (www.biointerchange.org/gfvo#Process)

# File lib/biointerchange/gfvo.rb, line 618
def self.Process
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Process')
end
ProteinSequence() click to toggle source

A protein sequence is a peptide sequence which represents the primary structure of a protein. (www.biointerchange.org/gfvo#ProteinSequence)

# File lib/biointerchange/gfvo.rb, line 624
def self.ProteinSequence
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ProteinSequence')
end
Quality() click to toggle source

Quality is a specific attribute that is strongly associated with an entity, but whose values are varying and disjunct. Qualities are finite enumerations, such as sex (“Female”, “Male”, “Hermaphrodite”), heritage (“Maternal”, “Paternal”), but they also make use of the “hasValue” datatype property such as “Coding Frame Offset” (either “0”, “1” or “2”). (www.biointerchange.org/gfvo#Quality)

# File lib/biointerchange/gfvo.rb, line 630
def self.Quality
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Quality')
end
Quantity() click to toggle source

A property of a phenomenon, body, or substance, where the property has a magnitude that can be expressed by means of a number and a reference. This class is typically not directly instantiated, but instead, its subclasses “Allele Frequency”, “Average Coverage”, etc. are used. (www.biointerchange.org/gfvo#Quantity)

# File lib/biointerchange/gfvo.rb, line 636
def self.Quantity
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Quantity')
end
RNASequencing() click to toggle source

Information about features and variants is based on RNA sequencing. (www.biointerchange.org/gfvo#RNASequencing)

# File lib/biointerchange/gfvo.rb, line 642
def self.RNASequencing
  return RDF::URI.new('http://www.biointerchange.org/gfvo#RNASequencing')
end
ReferenceSequence() click to toggle source

Denotes the reference sequence of a feature. The reference sequence is of importance when dealing with genomic variation data, which is expressed by the “Variant” class. (www.biointerchange.org/gfvo#ReferenceSequence)

# File lib/biointerchange/gfvo.rb, line 648
def self.ReferenceSequence
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ReferenceSequence')
end
ReferenceSequenceGap() click to toggle source

Denotes a gap in the reference sequence for an alignment. (www.biointerchange.org/gfvo#ReferenceSequenceGap)

# File lib/biointerchange/gfvo.rb, line 654
def self.ReferenceSequenceGap
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ReferenceSequenceGap')
end
ReverseReferenceSequenceFrameshift() click to toggle source

Denotes a frameshift backwards (reverse) in the reference sequence. (www.biointerchange.org/gfvo#ReverseReferenceSequenceFrameshift)

# File lib/biointerchange/gfvo.rb, line 660
def self.ReverseReferenceSequenceFrameshift
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ReverseReferenceSequenceFrameshift')
end
Sample() click to toggle source

A sample is a limited quantity of a chemical entity of some sort, which is typically used (destructively/non-desctructively) in a scientific analysis or test. (www.biointerchange.org/gfvo#Sample)

# File lib/biointerchange/gfvo.rb, line 666
def self.Sample
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Sample')
end
Scaffold() click to toggle source

A scaffold is the aggregation of multiple contigs to form a larger continuous sequencing region. (www.biointerchange.org/gfvo#Scaffold)

# File lib/biointerchange/gfvo.rb, line 672
def self.Scaffold
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Scaffold')
end
Score() click to toggle source

A measure that permits the ranking of entities. (www.biointerchange.org/gfvo#Score)

# File lib/biointerchange/gfvo.rb, line 678
def self.Score
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Score')
end
Sequence() click to toggle source

A sequence provides information about any biopolymer sequences. Specialized subclasses are provided to denote specialized instances of sequences, such as “Codon Sequence”, “Reference Sequence”, “Protein Sequence”, etc. (www.biointerchange.org/gfvo#Sequence)

# File lib/biointerchange/gfvo.rb, line 684
def self.Sequence
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Sequence')
end
SequenceAlignment() click to toggle source

A sequence alignment denotes the congruence of two sequences. In GFF3, a sequence alignment can be a nucleotide-to-nucleotide or protein-to-nucleotide alignment (see “The Gap Attribute”, sequenceontology.org/resources/gff3.html). “Alignment Operation” class instances denote the actual steps that the constitute the sequence alignment. (www.biointerchange.org/gfvo#SequenceAlignment)

# File lib/biointerchange/gfvo.rb, line 691
def self.SequenceAlignment
  return RDF::URI.new('http://www.biointerchange.org/gfvo#SequenceAlignment')
end
SequenceAlignmentOperation() click to toggle source

A sequence alignment operation captures the type of alignment (see “Sequence Alignment”) between a reference sequence and target sequence. Note that an “Alignment Operation” is situated in a linked list, where the order of the alignment operations is of significance. (www.biointerchange.org/gfvo#SequenceAlignmentOperation)

# File lib/biointerchange/gfvo.rb, line 697
def self.SequenceAlignmentOperation
  return RDF::URI.new('http://www.biointerchange.org/gfvo#SequenceAlignmentOperation')
end
SequenceVariant() click to toggle source

Describing specific sequence alterations of a genomic feature. A variant is related to “Reference” class instances, which denote the sequence that serves as a basis for sequence alteration comparisons. (www.biointerchange.org/gfvo#SequenceVariant)

# File lib/biointerchange/gfvo.rb, line 703
def self.SequenceVariant
  return RDF::URI.new('http://www.biointerchange.org/gfvo#SequenceVariant')
end
SequencedIndividual() click to toggle source

Aggregated sequencing information for a particular individual. (www.biointerchange.org/gfvo#SequencedIndividual)

# File lib/biointerchange/gfvo.rb, line 709
def self.SequencedIndividual
  return RDF::URI.new('http://www.biointerchange.org/gfvo#SequencedIndividual')
end
SequencingTechnologyPlatform() click to toggle source

Details about the sequencing/microarray technology used to gather the data in a set. (www.biointerchange.org/gfvo#SequencingTechnologyPlatform)

# File lib/biointerchange/gfvo.rb, line 715
def self.SequencingTechnologyPlatform
  return RDF::URI.new('http://www.biointerchange.org/gfvo#SequencingTechnologyPlatform')
end
Sex() click to toggle source

Biological sex of an individual. (www.biointerchange.org/gfvo#Sex)

# File lib/biointerchange/gfvo.rb, line 721
def self.Sex
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Sex')
end
SomaticCell() click to toggle source

The somatic feature class captures information about genomic sequence features arising from somatic cells. (www.biointerchange.org/gfvo#SomaticCell)

# File lib/biointerchange/gfvo.rb, line 727
def self.SomaticCell
  return RDF::URI.new('http://www.biointerchange.org/gfvo#SomaticCell')
end
Span() click to toggle source

A span is an attribute denoting the number of nucleotides or peptides that an entity covers. This is directly used in conjunction with “Sequence Alignment Operation” subclasses, e.g. to express the number of nucleotides a sequence alignment match ranges over. (www.biointerchange.org/gfvo#Span)

# File lib/biointerchange/gfvo.rb, line 733
def self.Span
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Span')
end
TargetSequenceGap() click to toggle source

Denotes a gap in the target sequence for an alignment. (www.biointerchange.org/gfvo#TargetSequenceGap)

# File lib/biointerchange/gfvo.rb, line 739
def self.TargetSequenceGap
  return RDF::URI.new('http://www.biointerchange.org/gfvo#TargetSequenceGap')
end
TotalNumber_ofReads() click to toggle source

Total number of reads covering a feature or variant. (www.biointerchange.org/gfvo#TotalNumberOfReads)

# File lib/biointerchange/gfvo.rb, line 745
def self.TotalNumber_ofReads
  return RDF::URI.new('http://www.biointerchange.org/gfvo#TotalNumberOfReads')
end
VariantCalling() click to toggle source

Denotes the technique of calling genomic feature variants in a genome assembly. (www.biointerchange.org/gfvo#VariantCalling)

# File lib/biointerchange/gfvo.rb, line 751
def self.VariantCalling
  return RDF::URI.new('http://www.biointerchange.org/gfvo#VariantCalling')
end
Version() click to toggle source

A version names a release of a software, dataset, or other resource. A versioned resource is not necessarily public. (www.biointerchange.org/gfvo#Version)

# File lib/biointerchange/gfvo.rb, line 757
def self.Version
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Version')
end
WatsonCrickHelix() click to toggle source

Helical structure as first proposed by Watson and Crick.

Can be used to indicate a false “Is_circular” attribute in GFF3 and GVF. (www.biointerchange.org/gfvo#WatsonCrickHelix)

# File lib/biointerchange/gfvo.rb, line 765
def self.WatsonCrickHelix
  return RDF::URI.new('http://www.biointerchange.org/gfvo#WatsonCrickHelix')
end
Zygosity() click to toggle source

Zygosity denotes the similarities of a specific allele in the genome of an organism. (www.biointerchange.org/gfvo#Zygosity)

# File lib/biointerchange/gfvo.rb, line 771
def self.Zygosity
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Zygosity')
end
describes() click to toggle source

Links to an entity for which supportive information is being provided. (www.biointerchange.org/gfvo#describes)

# File lib/biointerchange/gfvo.rb, line 8
def self.describes
  return RDF::URI.new('http://www.biointerchange.org/gfvo#describes')
end
has_annotation() click to toggle source

Links to additional annotations about an entity. (www.biointerchange.org/gfvo#hasAnnotation)

# File lib/biointerchange/gfvo.rb, line 14
def self.has_annotation
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasAnnotation')
end
has_attribute() click to toggle source

Links out to aggregate information for an entity. (www.biointerchange.org/gfvo#hasAttribute)

# File lib/biointerchange/gfvo.rb, line 20
def self.has_attribute
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasAttribute')
end
has_evidence() click to toggle source

References an entity or resource that provides supporting/refuting evidence. (www.biointerchange.org/gfvo#hasEvidence)

# File lib/biointerchange/gfvo.rb, line 26
def self.has_evidence
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasEvidence')
end
has_first_part() click to toggle source

Denotes the first entity of an ordered part relationship. (www.biointerchange.org/gfvo#hasFirstPart)

# File lib/biointerchange/gfvo.rb, line 32
def self.has_first_part
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasFirstPart')
end
has_identifier() click to toggle source

Links out to an identifier. (www.biointerchange.org/gfvo#hasIdentifier)

# File lib/biointerchange/gfvo.rb, line 38
def self.has_identifier
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasIdentifier')
end
has_input() click to toggle source

Links out to an entity that is the input of a “Process” subclass. (www.biointerchange.org/gfvo#hasInput)

# File lib/biointerchange/gfvo.rb, line 44
def self.has_input
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasInput')
end
has_last_part() click to toggle source

Denotes the last entity of an ordered part relationship. (www.biointerchange.org/gfvo#hasLastPart)

# File lib/biointerchange/gfvo.rb, line 50
def self.has_last_part
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasLastPart')
end
has_member() click to toggle source

Denotes membership for “Collection”, “Catalog” and “File” instances. (www.biointerchange.org/gfvo#hasMember)

# File lib/biointerchange/gfvo.rb, line 56
def self.has_member
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasMember')
end
has_ordered_part() click to toggle source

Denotes a compositional relationship to other entities, where the ordering of the composition of entities carries meaning. (www.biointerchange.org/gfvo#hasOrderedPart)

# File lib/biointerchange/gfvo.rb, line 62
def self.has_ordered_part
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasOrderedPart')
end
has_output() click to toggle source

Links out to an entity that is the output of a “Process” subclass. (www.biointerchange.org/gfvo#hasOutput)

# File lib/biointerchange/gfvo.rb, line 68
def self.has_output
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasOutput')
end
has_parent?(uri, parent) click to toggle source

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.

# File lib/biointerchange/gfvo.rb, line 1193
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
has_part() click to toggle source

Denotes a compositional relationship to other entities. (www.biointerchange.org/gfvo#hasPart)

# File lib/biointerchange/gfvo.rb, line 74
def self.has_part
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasPart')
end
has_participant() click to toggle source

Denotes the participation of other entities in processes. (www.biointerchange.org/gfvo#hasParticipant)

# File lib/biointerchange/gfvo.rb, line 80
def self.has_participant
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasParticipant')
end
has_quality() click to toggle source

Links out to an entity that provides qualitative information. (www.biointerchange.org/gfvo#hasQuality)

# File lib/biointerchange/gfvo.rb, line 86
def self.has_quality
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasQuality')
end
has_source() click to toggle source

Denotes information origin. (www.biointerchange.org/gfvo#hasSource)

# File lib/biointerchange/gfvo.rb, line 92
def self.has_source
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasSource')
end
has_value() click to toggle source

Representation of any literal that is associated with a GFVO class instance. Domain restrictions might apply. For example, “Codon Sequence” entities restrict “has value” to be a non-empty string consisting of A, C, G, or T letters, and whose length is a multiple of 3. (www.biointerchange.org/gfvo#hasValue)

# File lib/biointerchange/gfvo.rb, line 202
def self.has_value
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasValue')
end
is_about() click to toggle source

References an entity about which information is provided for. (www.biointerchange.org/gfvo#isAbout)

# File lib/biointerchange/gfvo.rb, line 98
def self.is_about
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isAbout')
end
is_affected_by() click to toggle source

Denotes that an entity is affected by another entity. (www.biointerchange.org/gfvo#isAffectedBy)

# File lib/biointerchange/gfvo.rb, line 104
def self.is_affected_by
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isAffectedBy')
end
is_after() click to toggle source

Denotes the trailing occurrence or succession of the subject in regards to the object. (www.biointerchange.org/gfvo#isAfter)

# File lib/biointerchange/gfvo.rb, line 110
def self.is_after
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isAfter')
end
is_attribute_of() click to toggle source

Denotes that an entity is an attribute of the entity that this property links out to. (www.biointerchange.org/gfvo#isAttributeOf)

# File lib/biointerchange/gfvo.rb, line 116
def self.is_attribute_of
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isAttributeOf')
end
is_before() click to toggle source

Denotes the leading occurrence or precedence of the subject in regards to the object. (www.biointerchange.org/gfvo#isBefore)

# File lib/biointerchange/gfvo.rb, line 122
def self.is_before
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isBefore')
end
is_class?(uri) click to toggle source

Determines whether the given URI is a class.

uri

URI that is tested for being a class

# File lib/biointerchange/gfvo.rb, line 891
def self.is_class?(uri)
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Alias') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#AlleleFrequency') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#AminoAcid') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#AncestralSequence') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ArrayComparativeGenomicHybridization') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Attribute') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#AverageCoverage') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#BiologicalEntity') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#BiopolymerSequencing') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Breakpoint') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Catalog') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Cell') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ChemicalEntity') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Chromosome') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#CircularHelix') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#CodingFrameOffset') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#CodonSequence') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Collection') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Comment') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Contig') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Coverage') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#DNAMicroarray') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#DNASequence') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#DNASequencing') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ExperimentalMethod') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ExternalReference') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Feature') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Female') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#File') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ForwardReferenceSequenceFrameshift') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#FragmentReadPlatform') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#FunctionalSpecification') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#GameticPhase') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Genome') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#GenomeAnalysis') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#GenomicAscertainingMethod') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Genotype') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Genotyping') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#GermlineCell') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#HelixStructure') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Hemizygous') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Heritage') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Hermaphrodite') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Heterozygous') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Homozygous') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Identifier') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#InformationContentEntity') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Interaction') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Label') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Landmark') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Likelihood') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Locus') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Male') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Match') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#MaterialEntity') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#MaternalHeritage') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#MobileElementSequenceVariant') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Name') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Note') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#NumberOfReads') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Object') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#PairedEndReadPlatform') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#PaternalHeritage') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#PeptideSequence') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Phenotype') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#PhredScore') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#PrenatalCell') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Process') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ProteinSequence') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Quality') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Quantity') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#RNASequencing') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ReferenceSequence') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ReferenceSequenceGap') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ReverseReferenceSequenceFrameshift') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Sample') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Scaffold') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Score') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Sequence') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#SequenceAlignment') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#SequenceAlignmentOperation') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#SequenceVariant') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#SequencedIndividual') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#SequencingTechnologyPlatform') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Sex') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#SomaticCell') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Span') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#TargetSequenceGap') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#TotalNumberOfReads') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#VariantCalling') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Version') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#WatsonCrickHelix') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Zygosity') then
    return true
  end
  return false
end
is_created_by() click to toggle source

Denotes the process or method that created an entity. (www.biointerchange.org/gfvo#isCreatedBy)

# File lib/biointerchange/gfvo.rb, line 128
def self.is_created_by
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isCreatedBy')
end
is_datatype_property?(uri) click to toggle source

Determines whether the given URI is a datatype property.

uri

URI that is tested for being a datatype property

# File lib/biointerchange/gfvo.rb, line 881
def self.is_datatype_property?(uri)
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasValue') then
    return true
  end
  return false
end
is_described_by() click to toggle source

Provides a description of the subject via reference to an object that provides further information on the subject. (www.biointerchange.org/gfvo#isDescribedBy)

# File lib/biointerchange/gfvo.rb, line 134
def self.is_described_by
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isDescribedBy')
end
is_located_on() click to toggle source

Denotes the location of genomic feature on a landmark. (www.biointerchange.org/gfvo#isLocatedOn)

# File lib/biointerchange/gfvo.rb, line 140
def self.is_located_on
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isLocatedOn')
end
is_named_individual?(uri) click to toggle source

Determines whether the given URI is a named individual.

uri

URI that is tested for being a named individual

# File lib/biointerchange/gfvo.rb, line 1177
def self.is_named_individual?(uri)
  return false
end
is_object_property?(uri) click to toggle source

Determines whether the given URI is an object property.

uri

URI that is tested for being an object property

# File lib/biointerchange/gfvo.rb, line 778
def self.is_object_property?(uri)
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#describes') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasAnnotation') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasAttribute') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasEvidence') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasFirstPart') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasIdentifier') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasInput') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasLastPart') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasMember') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasOrderedPart') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasOutput') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasPart') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasParticipant') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasQuality') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasSource') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isAbout') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isAffectedBy') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isAfter') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isAttributeOf') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isBefore') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isCreatedBy') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isDescribedBy') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isLocatedOn') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isPartOf') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isParticipantIn') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isRefutedBy') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isSourceOf') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isSpatiotemporallyRelatedTo') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isSupportedBy') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isTemporarilyPartOf') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#references') then
    return true
  end
  if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#refersTo') then
    return true
  end
  return false
end
is_part_of() click to toggle source

Denotes that an entity is an intrinsic component of an encapsulating entity. (www.biointerchange.org/gfvo#isPartOf)

# File lib/biointerchange/gfvo.rb, line 146
def self.is_part_of
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isPartOf')
end
is_participant_in() click to toggle source

Denotes participation with another entity. (www.biointerchange.org/gfvo#isParticipantIn)

# File lib/biointerchange/gfvo.rb, line 152
def self.is_participant_in
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isParticipantIn')
end
is_refuted_by() click to toggle source

References an entity or resource that provides refuting evidence. (www.biointerchange.org/gfvo#isRefutedBy)

# File lib/biointerchange/gfvo.rb, line 158
def self.is_refuted_by
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isRefutedBy')
end
is_source_of() click to toggle source

Denotes that an entity is the source of the entity that this property links out to. (www.biointerchange.org/gfvo#isSourceOf)

# File lib/biointerchange/gfvo.rb, line 164
def self.is_source_of
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isSourceOf')
end
is_supported_by() click to toggle source

References an entity or resource that provides supporting evidence. (www.biointerchange.org/gfvo#isSupportedBy)

# File lib/biointerchange/gfvo.rb, line 176
def self.is_supported_by
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isSupportedBy')
end
is_temporarily_part_of() click to toggle source

Denotes a temporarily constraint “isPartOf” relationship. The temporal restriction expresses that the relationship is not universally true.

This property can be used to express “Derives_from” relations in GFF3. (www.biointerchange.org/gfvo#isTemporarilyPartOf)

# File lib/biointerchange/gfvo.rb, line 184
def self.is_temporarily_part_of
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isTemporarilyPartOf')
end
references() click to toggle source

References another entity or resource. (www.biointerchange.org/gfvo#references)

# File lib/biointerchange/gfvo.rb, line 190
def self.references
  return RDF::URI.new('http://www.biointerchange.org/gfvo#references')
end
refers_to() click to toggle source

References an entity, where additional information is provided to augment the reference. (www.biointerchange.org/gfvo#refersTo)

# File lib/biointerchange/gfvo.rb, line 196
def self.refers_to
  return RDF::URI.new('http://www.biointerchange.org/gfvo#refersTo')
end
with_parent(uris, parent) click to toggle source

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.

# File lib/biointerchange/gfvo.rb, line 1185
def self.with_parent(uris, parent)
  return uris.select { |uri| has_parent?(uri, parent) }
end