Class: BioInterchange::GFVO

Inherits:
Object
  • Object
show all
Defined in:
lib/biointerchange/gfvo.rb

Class Method Summary collapse

Class Method Details

.Alias ⇒ Object

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



208
209
210
 
# File 'lib/biointerchange/gfvo.rb', line 208

def self.Alias
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Alias')
end

.AlleleFrequency ⇒ Object

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



214
215
216
 
# File 'lib/biointerchange/gfvo.rb', line 214

def self.AlleleFrequency
  return RDF::URI.new('http://www.biointerchange.org/gfvo#AlleleFrequency')
end

.AminoAcid ⇒ Object

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



220
221
222
 
# File 'lib/biointerchange/gfvo.rb', line 220

def self.AminoAcid
  return RDF::URI.new('http://www.biointerchange.org/gfvo#AminoAcid')
end

.AncestralSequence ⇒ Object

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



226
227
228
 
# File 'lib/biointerchange/gfvo.rb', line 226

def self.AncestralSequence
  return RDF::URI.new('http://www.biointerchange.org/gfvo#AncestralSequence')
end

.ArrayComparativeGenomicHybridization ⇒ Object

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



232
233
234
 
# File 'lib/biointerchange/gfvo.rb', line 232

def self.ArrayComparativeGenomicHybridization
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ArrayComparativeGenomicHybridization')
end

.Attribute ⇒ Object

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)



240
241
242
 
# File 'lib/biointerchange/gfvo.rb', line 240

def self.Attribute
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Attribute')
end

.AverageCoverage ⇒ Object

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)



246
247
248
 
# File 'lib/biointerchange/gfvo.rb', line 246

def self.AverageCoverage
  return RDF::URI.new('http://www.biointerchange.org/gfvo#AverageCoverage')
end

.BiologicalEntity ⇒ Object

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)



252
253
254
 
# File 'lib/biointerchange/gfvo.rb', line 252

def self.BiologicalEntity
  return RDF::URI.new('http://www.biointerchange.org/gfvo#BiologicalEntity')
end

.BiopolymerSequencing ⇒ Object

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



258
259
260
 
# File 'lib/biointerchange/gfvo.rb', line 258

def self.BiopolymerSequencing
  return RDF::URI.new('http://www.biointerchange.org/gfvo#BiopolymerSequencing')
end

.Breakpoint ⇒ Object

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)



264
265
266
 
# File 'lib/biointerchange/gfvo.rb', line 264

def self.Breakpoint
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Breakpoint')
end

.Catalog ⇒ Object

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



270
271
272
 
# File 'lib/biointerchange/gfvo.rb', line 270

def self.Catalog
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Catalog')
end

.Cell ⇒ Object

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)



276
277
278
 
# File 'lib/biointerchange/gfvo.rb', line 276

def self.Cell
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Cell')
end

.ChemicalEntity ⇒ Object

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)



282
283
284
 
# File 'lib/biointerchange/gfvo.rb', line 282

def self.ChemicalEntity
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ChemicalEntity')
end

.Chromosome ⇒ Object

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)



288
289
290
 
# File 'lib/biointerchange/gfvo.rb', line 288

def self.Chromosome
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Chromosome')
end

.CircularHelix ⇒ Object

A circular helix structure.

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



296
297
298
 
# File 'lib/biointerchange/gfvo.rb', line 296

def self.CircularHelix
  return RDF::URI.new('http://www.biointerchange.org/gfvo#CircularHelix')
end

.CodingFrameOffset ⇒ Object

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)



302
303
304
 
# File 'lib/biointerchange/gfvo.rb', line 302

def self.CodingFrameOffset
  return RDF::URI.new('http://www.biointerchange.org/gfvo#CodingFrameOffset')
end

.CodonSequence ⇒ Object

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)



308
309
310
 
# File 'lib/biointerchange/gfvo.rb', line 308

def self.CodonSequence
  return RDF::URI.new('http://www.biointerchange.org/gfvo#CodonSequence')
end

.Collection ⇒ Object

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)



314
315
316
 
# File 'lib/biointerchange/gfvo.rb', line 314

def self.Collection
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Collection')
end

.Comment ⇒ Object

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)



320
321
322
 
# File 'lib/biointerchange/gfvo.rb', line 320

def self.Comment
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Comment')
end

.Contig ⇒ Object

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



326
327
328
 
# File 'lib/biointerchange/gfvo.rb', line 326

def self.Contig
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Contig')
end

.Coverage ⇒ Object

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



332
333
334
 
# File 'lib/biointerchange/gfvo.rb', line 332

def self.Coverage
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Coverage')
end

.describes ⇒ Object

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



8
9
10
 
# File 'lib/biointerchange/gfvo.rb', line 8

def self.describes
  return RDF::URI.new('http://www.biointerchange.org/gfvo#describes')
end

.DNAMicroarray ⇒ Object

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



338
339
340
 
# File 'lib/biointerchange/gfvo.rb', line 338

def self.DNAMicroarray
  return RDF::URI.new('http://www.biointerchange.org/gfvo#DNAMicroarray')
end

.DNASequence ⇒ Object

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



344
345
346
 
# File 'lib/biointerchange/gfvo.rb', line 344

def self.DNASequence
  return RDF::URI.new('http://www.biointerchange.org/gfvo#DNASequence')
end

.DNASequencing ⇒ Object

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



350
351
352
 
# File 'lib/biointerchange/gfvo.rb', line 350

def self.DNASequencing
  return RDF::URI.new('http://www.biointerchange.org/gfvo#DNASequencing')
end

.ExperimentalMethod ⇒ Object

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)



356
357
358
 
# File 'lib/biointerchange/gfvo.rb', line 356

def self.ExperimentalMethod
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ExperimentalMethod')
end

.ExternalReference ⇒ Object

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



362
363
364
 
# File 'lib/biointerchange/gfvo.rb', line 362

def self.ExternalReference
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ExternalReference')
end

.Feature ⇒ Object

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)



368
369
370
 
# File 'lib/biointerchange/gfvo.rb', line 368

def self.Feature
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Feature')
end

.Female ⇒ Object

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



374
375
376
 
# File 'lib/biointerchange/gfvo.rb', line 374

def self.Female
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Female')
end

.File ⇒ Object

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)



380
381
382
 
# File 'lib/biointerchange/gfvo.rb', line 380

def self.File
  return RDF::URI.new('http://www.biointerchange.org/gfvo#File')
end

.ForwardReferenceSequenceFrameshift ⇒ Object

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



386
387
388
 
# File 'lib/biointerchange/gfvo.rb', line 386

def self.ForwardReferenceSequenceFrameshift
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ForwardReferenceSequenceFrameshift')
end

.FragmentReadPlatform ⇒ Object

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



392
393
394
 
# File 'lib/biointerchange/gfvo.rb', line 392

def self.FragmentReadPlatform
  return RDF::URI.new('http://www.biointerchange.org/gfvo#FragmentReadPlatform')
end

.FunctionalSpecification ⇒ Object

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



398
399
400
 
# File 'lib/biointerchange/gfvo.rb', line 398

def self.FunctionalSpecification
  return RDF::URI.new('http://www.biointerchange.org/gfvo#FunctionalSpecification')
end

.GameticPhase ⇒ Object

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)



404
405
406
 
# File 'lib/biointerchange/gfvo.rb', line 404

def self.GameticPhase
  return RDF::URI.new('http://www.biointerchange.org/gfvo#GameticPhase')
end

.Genome ⇒ Object

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)



410
411
412
 
# File 'lib/biointerchange/gfvo.rb', line 410

def self.Genome
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Genome')
end

.GenomeAnalysis ⇒ Object

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



416
417
418
 
# File 'lib/biointerchange/gfvo.rb', line 416

def self.GenomeAnalysis
  return RDF::URI.new('http://www.biointerchange.org/gfvo#GenomeAnalysis')
end

.GenomicAscertainingMethod ⇒ Object

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



422
423
424
 
# File 'lib/biointerchange/gfvo.rb', line 422

def self.GenomicAscertainingMethod
  return RDF::URI.new('http://www.biointerchange.org/gfvo#GenomicAscertainingMethod')
end

.Genotype ⇒ Object

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)



432
433
434
 
# File 'lib/biointerchange/gfvo.rb', line 432

def self.Genotype
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Genotype')
end

.Genotyping ⇒ Object

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)



438
439
440
 
# File 'lib/biointerchange/gfvo.rb', line 438

def self.Genotyping
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Genotyping')
end

.GermlineCell ⇒ Object

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



444
445
446
 
# File 'lib/biointerchange/gfvo.rb', line 444

def self.GermlineCell
  return RDF::URI.new('http://www.biointerchange.org/gfvo#GermlineCell')
end

.has_annotation ⇒ Object

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



14
15
16
 
# File 'lib/biointerchange/gfvo.rb', line 14

def self.has_annotation
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasAnnotation')
end

.has_attribute ⇒ Object

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



20
21
22
 
# File 'lib/biointerchange/gfvo.rb', line 20

def self.has_attribute
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasAttribute')
end

.has_evidence ⇒ Object

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



26
27
28
 
# 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 ⇒ Object

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



32
33
34
 
# 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 ⇒ Object

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



38
39
40
 
# File 'lib/biointerchange/gfvo.rb', line 38

def self.has_identifier
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasIdentifier')
end

.has_input ⇒ Object

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



44
45
46
 
# 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 ⇒ Object

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



50
51
52
 
# 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 ⇒ Object

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



56
57
58
 
# 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 ⇒ Object

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



62
63
64
 
# 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 ⇒ Object

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



68
69
70
 
# 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) ⇒ Boolean

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.

Returns:

  • (Boolean) 


1193
1194
1195
1196
1197
1198
1199
1200
1201
 
# 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 ⇒ Object

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



74
75
76
 
# File 'lib/biointerchange/gfvo.rb', line 74

def self.has_part
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasPart')
end

.has_participant ⇒ Object

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



80
81
82
 
# File 'lib/biointerchange/gfvo.rb', line 80

def self.has_participant
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasParticipant')
end

.has_quality ⇒ Object

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



86
87
88
 
# File 'lib/biointerchange/gfvo.rb', line 86

def self.has_quality
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasQuality')
end

.has_source ⇒ Object

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



92
93
94
 
# File 'lib/biointerchange/gfvo.rb', line 92

def self.has_source
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasSource')
end

.has_value ⇒ Object

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)



202
203
204
 
# File 'lib/biointerchange/gfvo.rb', line 202

def self.has_value
  return RDF::URI.new('http://www.biointerchange.org/gfvo#hasValue')
end

.HelixStructure ⇒ Object

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



450
451
452
 
# File 'lib/biointerchange/gfvo.rb', line 450

def self.HelixStructure
  return RDF::URI.new('http://www.biointerchange.org/gfvo#HelixStructure')
end

.Hemizygous ⇒ Object

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



456
457
458
 
# File 'lib/biointerchange/gfvo.rb', line 456

def self.Hemizygous
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Hemizygous')
end

.Heritage ⇒ Object

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)



462
463
464
 
# File 'lib/biointerchange/gfvo.rb', line 462

def self.Heritage
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Heritage')
end

.Hermaphrodite ⇒ Object

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



468
469
470
 
# File 'lib/biointerchange/gfvo.rb', line 468

def self.Hermaphrodite
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Hermaphrodite')
end

.Heterozygous ⇒ Object

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



474
475
476
 
# File 'lib/biointerchange/gfvo.rb', line 474

def self.Heterozygous
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Heterozygous')
end

.Homozygous ⇒ Object

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



480
481
482
 
# File 'lib/biointerchange/gfvo.rb', line 480

def self.Homozygous
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Homozygous')
end

.Identifier ⇒ Object

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)



486
487
488
 
# File 'lib/biointerchange/gfvo.rb', line 486

def self.Identifier
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Identifier')
end

.InformationContentEntity ⇒ Object

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



492
493
494
 
# File 'lib/biointerchange/gfvo.rb', line 492

def self.InformationContentEntity
  return RDF::URI.new('http://www.biointerchange.org/gfvo#InformationContentEntity')
end

.Interaction ⇒ Object

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



498
499
500
 
# File 'lib/biointerchange/gfvo.rb', line 498

def self.Interaction
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Interaction')
end

.is_about ⇒ Object

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



98
99
100
 
# 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 ⇒ Object

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



104
105
106
 
# 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 ⇒ Object

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



110
111
112
 
# 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 ⇒ Object

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



116
117
118
 
# 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 ⇒ Object

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



122
123
124
 
# 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) ⇒ Boolean

Determines whether the given URI is a class.

uri

URI that is tested for being a class

Returns:

  • (Boolean) 


891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
 
# 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 ⇒ Object

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



128
129
130
 
# 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) ⇒ Boolean

Determines whether the given URI is a datatype property.

uri

URI that is tested for being a datatype property

Returns:

  • (Boolean) 


881
882
883
884
885
886
 
# 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 ⇒ Object

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



134
135
136
 
# 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 ⇒ Object

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



140
141
142
 
# 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) ⇒ Boolean

Determines whether the given URI is a named individual.

uri

URI that is tested for being a named individual

Returns:

  • (Boolean) 


1177
1178
1179
 
# File 'lib/biointerchange/gfvo.rb', line 1177

def self.is_named_individual?(uri)
  return false
end

.is_object_property?(uri) ⇒ Boolean

Determines whether the given URI is an object property.

uri

URI that is tested for being an object property

Returns:

  • (Boolean) 


778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
 
# 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 ⇒ Object

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



146
147
148
 
# 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 ⇒ Object

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



152
153
154
 
# 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 ⇒ Object

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



158
159
160
 
# 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 ⇒ Object

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



164
165
166
 
# File 'lib/biointerchange/gfvo.rb', line 164

def self.is_source_of
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isSourceOf')
end

.is_spatiotemporally_related_to ⇒ Object

Denotes spatio-temporal relations to other entities. (www.biointerchange.org/gfvo#isSpatiotemporallyRelatedTo)



170
171
172
 
# File 'lib/biointerchange/gfvo.rb', line 170

def self.is_spatiotemporally_related_to
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isSpatiotemporallyRelatedTo')
end

.is_supported_by ⇒ Object

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



176
177
178
 
# 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 ⇒ Object

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)



184
185
186
 
# File 'lib/biointerchange/gfvo.rb', line 184

def self.is_temporarily_part_of
  return RDF::URI.new('http://www.biointerchange.org/gfvo#isTemporarilyPartOf')
end

.Label ⇒ Object

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)



504
505
506
 
# File 'lib/biointerchange/gfvo.rb', line 504

def self.Label
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Label')
end

.Landmark ⇒ Object

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)



510
511
512
 
# File 'lib/biointerchange/gfvo.rb', line 510

def self.Landmark
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Landmark')
end

.Likelihood ⇒ Object

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



516
517
518
 
# File 'lib/biointerchange/gfvo.rb', line 516

def self.Likelihood
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Likelihood')
end

.Locus ⇒ Object

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



522
523
524
 
# File 'lib/biointerchange/gfvo.rb', line 522

def self.Locus
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Locus')
end

.Male ⇒ Object

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



528
529
530
 
# File 'lib/biointerchange/gfvo.rb', line 528

def self.Male
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Male')
end

.Match ⇒ Object

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



534
535
536
 
# File 'lib/biointerchange/gfvo.rb', line 534

def self.Match
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Match')
end

.MaterialEntity ⇒ Object

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)



540
541
542
 
# File 'lib/biointerchange/gfvo.rb', line 540

def self.MaterialEntity
  return RDF::URI.new('http://www.biointerchange.org/gfvo#MaterialEntity')
end

.MaternalHeritage ⇒ Object

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



546
547
548
 
# File 'lib/biointerchange/gfvo.rb', line 546

def self.MaternalHeritage
  return RDF::URI.new('http://www.biointerchange.org/gfvo#MaternalHeritage')
end

.MobileElementSequenceVariant ⇒ Object

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



552
553
554
 
# File 'lib/biointerchange/gfvo.rb', line 552

def self.MobileElementSequenceVariant
  return RDF::URI.new('http://www.biointerchange.org/gfvo#MobileElementSequenceVariant')
end

.Name ⇒ Object

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)



558
559
560
 
# File 'lib/biointerchange/gfvo.rb', line 558

def self.Name
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Name')
end

.Note ⇒ Object

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



564
565
566
 
# File 'lib/biointerchange/gfvo.rb', line 564

def self.Note
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Note')
end

.Number_ofReads ⇒ Object

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



570
571
572
 
# File 'lib/biointerchange/gfvo.rb', line 570

def self.Number_ofReads
  return RDF::URI.new('http://www.biointerchange.org/gfvo#NumberOfReads')
end

.Object ⇒ Object

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)



576
577
578
 
# File 'lib/biointerchange/gfvo.rb', line 576

def self.Object
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Object')
end

.PairedEndReadPlatform ⇒ Object

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



582
583
584
 
# File 'lib/biointerchange/gfvo.rb', line 582

def self.PairedEndReadPlatform
  return RDF::URI.new('http://www.biointerchange.org/gfvo#PairedEndReadPlatform')
end

.PaternalHeritage ⇒ Object

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



588
589
590
 
# File 'lib/biointerchange/gfvo.rb', line 588

def self.PaternalHeritage
  return RDF::URI.new('http://www.biointerchange.org/gfvo#PaternalHeritage')
end

.PeptideSequence ⇒ Object

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)



594
595
596
 
# File 'lib/biointerchange/gfvo.rb', line 594

def self.PeptideSequence
  return RDF::URI.new('http://www.biointerchange.org/gfvo#PeptideSequence')
end

.Phenotype ⇒ Object

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)



600
601
602
 
# File 'lib/biointerchange/gfvo.rb', line 600

def self.Phenotype
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Phenotype')
end

.PhredScore ⇒ Object

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



606
607
608
 
# File 'lib/biointerchange/gfvo.rb', line 606

def self.PhredScore
  return RDF::URI.new('http://www.biointerchange.org/gfvo#PhredScore')
end

.PrenatalCell ⇒ Object

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)



612
613
614
 
# File 'lib/biointerchange/gfvo.rb', line 612

def self.PrenatalCell
  return RDF::URI.new('http://www.biointerchange.org/gfvo#PrenatalCell')
end

.Process ⇒ Object

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)



618
619
620
 
# File 'lib/biointerchange/gfvo.rb', line 618

def self.Process
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Process')
end

.ProteinSequence ⇒ Object

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



624
625
626
 
# File 'lib/biointerchange/gfvo.rb', line 624

def self.ProteinSequence
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ProteinSequence')
end

.Quality ⇒ Object

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)



630
631
632
 
# File 'lib/biointerchange/gfvo.rb', line 630

def self.Quality
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Quality')
end

.Quantity ⇒ Object

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)



636
637
638
 
# File 'lib/biointerchange/gfvo.rb', line 636

def self.Quantity
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Quantity')
end

.references ⇒ Object

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



190
191
192
 
# File 'lib/biointerchange/gfvo.rb', line 190

def self.references
  return RDF::URI.new('http://www.biointerchange.org/gfvo#references')
end

.ReferenceSequence ⇒ Object

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)



648
649
650
 
# File 'lib/biointerchange/gfvo.rb', line 648

def self.ReferenceSequence
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ReferenceSequence')
end

.ReferenceSequenceGap ⇒ Object

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



654
655
656
 
# File 'lib/biointerchange/gfvo.rb', line 654

def self.ReferenceSequenceGap
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ReferenceSequenceGap')
end

.refers_to ⇒ Object

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



196
197
198
 
# File 'lib/biointerchange/gfvo.rb', line 196

def self.refers_to
  return RDF::URI.new('http://www.biointerchange.org/gfvo#refersTo')
end

.ReverseReferenceSequenceFrameshift ⇒ Object

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



660
661
662
 
# File 'lib/biointerchange/gfvo.rb', line 660

def self.ReverseReferenceSequenceFrameshift
  return RDF::URI.new('http://www.biointerchange.org/gfvo#ReverseReferenceSequenceFrameshift')
end

.RNASequencing ⇒ Object

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



642
643
644
 
# File 'lib/biointerchange/gfvo.rb', line 642

def self.RNASequencing
  return RDF::URI.new('http://www.biointerchange.org/gfvo#RNASequencing')
end

.Sample ⇒ Object

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)



666
667
668
 
# File 'lib/biointerchange/gfvo.rb', line 666

def self.Sample
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Sample')
end

.Scaffold ⇒ Object

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



672
673
674
 
# File 'lib/biointerchange/gfvo.rb', line 672

def self.Scaffold
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Scaffold')
end

.Score ⇒ Object

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



678
679
680
 
# File 'lib/biointerchange/gfvo.rb', line 678

def self.Score
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Score')
end

.Sequence ⇒ Object

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)



684
685
686
 
# File 'lib/biointerchange/gfvo.rb', line 684

def self.Sequence
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Sequence')
end

.SequenceAlignment ⇒ Object

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)



691
692
693
 
# File 'lib/biointerchange/gfvo.rb', line 691

def self.SequenceAlignment
  return RDF::URI.new('http://www.biointerchange.org/gfvo#SequenceAlignment')
end

.SequenceAlignmentOperation ⇒ Object

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)



697
698
699
 
# File 'lib/biointerchange/gfvo.rb', line 697

def self.SequenceAlignmentOperation
  return RDF::URI.new('http://www.biointerchange.org/gfvo#SequenceAlignmentOperation')
end

.SequencedIndividual ⇒ Object

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



709
710
711
 
# File 'lib/biointerchange/gfvo.rb', line 709

def self.SequencedIndividual
  return RDF::URI.new('http://www.biointerchange.org/gfvo#SequencedIndividual')
end

.SequenceVariant ⇒ Object

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)



703
704
705
 
# File 'lib/biointerchange/gfvo.rb', line 703

def self.SequenceVariant
  return RDF::URI.new('http://www.biointerchange.org/gfvo#SequenceVariant')
end

.SequencingTechnologyPlatform ⇒ Object

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



715
716
717
 
# File 'lib/biointerchange/gfvo.rb', line 715

def self.SequencingTechnologyPlatform
  return RDF::URI.new('http://www.biointerchange.org/gfvo#SequencingTechnologyPlatform')
end

.Sex ⇒ Object

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



721
722
723
 
# File 'lib/biointerchange/gfvo.rb', line 721

def self.Sex
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Sex')
end

.SomaticCell ⇒ Object

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



727
728
729
 
# File 'lib/biointerchange/gfvo.rb', line 727

def self.SomaticCell
  return RDF::URI.new('http://www.biointerchange.org/gfvo#SomaticCell')
end

.Span ⇒ Object

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)



733
734
735
 
# File 'lib/biointerchange/gfvo.rb', line 733

def self.Span
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Span')
end

.TargetSequenceGap ⇒ Object

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



739
740
741
 
# File 'lib/biointerchange/gfvo.rb', line 739

def self.TargetSequenceGap
  return RDF::URI.new('http://www.biointerchange.org/gfvo#TargetSequenceGap')
end

.TotalNumber_ofReads ⇒ Object

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



745
746
747
 
# File 'lib/biointerchange/gfvo.rb', line 745

def self.TotalNumber_ofReads
  return RDF::URI.new('http://www.biointerchange.org/gfvo#TotalNumberOfReads')
end

.VariantCalling ⇒ Object

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



751
752
753
 
# File 'lib/biointerchange/gfvo.rb', line 751

def self.VariantCalling
  return RDF::URI.new('http://www.biointerchange.org/gfvo#VariantCalling')
end

.Version ⇒ Object

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



757
758
759
 
# File 'lib/biointerchange/gfvo.rb', line 757

def self.Version
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Version')
end

.WatsonCrickHelix ⇒ Object

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)



765
766
767
 
# File 'lib/biointerchange/gfvo.rb', line 765

def self.WatsonCrickHelix
  return RDF::URI.new('http://www.biointerchange.org/gfvo#WatsonCrickHelix')
end

.with_parent(uris, parent) ⇒ Object

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.



1185
1186
1187
 
# File 'lib/biointerchange/gfvo.rb', line 1185

def self.with_parent(uris, parent)
  return uris.select { |uri| has_parent?(uri, parent) }
end

.Zygosity ⇒ Object

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



771
772
773
 
# File 'lib/biointerchange/gfvo.rb', line 771

def self.Zygosity
  return RDF::URI.new('http://www.biointerchange.org/gfvo#Zygosity')
end