biointerchange 1.0.1 → 1.0.2
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- checksums.yaml +4 -4
- data/.travis.yml +2 -4
- data/Gemfile +2 -3
- data/README.md +36 -22
- data/VERSION +1 -1
- data/examples/Felis_catus.gvf.gz +0 -0
- data/examples/Felis_catus_incl_consequences.vcf.gz +0 -0
- data/generators/rdfxml.rb +1 -1
- data/generators/tsv2rubyclass.rb +31 -0
- data/lib/biointerchange/core.rb +17 -5
- data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +591 -137
- data/lib/biointerchange/genomics/gff3_reader.rb +16 -3
- data/lib/biointerchange/genomics/gvf_reader.rb +1 -1
- data/lib/biointerchange/genomics/vcf_feature.rb +46 -0
- data/lib/biointerchange/genomics/vcf_feature_set.rb +14 -0
- data/lib/biointerchange/genomics/vcf_reader.rb +238 -0
- data/lib/biointerchange/gfvo.rb +689 -553
- data/lib/biointerchange/life_science_registry.rb +3595 -0
- data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb +33 -35
- data/lib/biointerchange/writer.rb +11 -16
- data/make.sh +4 -0
- data/spec/exceptions_spec.rb +1 -7
- data/spec/gff3_rdfwriter_spec.rb +2 -16
- data/spec/gvf_rdfwriter_spec.rb +2 -19
- data/spec/phylogenetics_spec.rb +1 -13
- data/spec/text_mining_pdfx_xml_reader_spec.rb +1 -13
- data/spec/text_mining_pubannos_json_reader_spec.rb +1 -14
- data/spec/text_mining_rdfwriter_spec.rb +8 -19
- data/test.sh +4 -0
- data/web/about.html +10 -14
- data/web/api.html +11 -13
- data/web/bootstrap/css/bootstrap-theme.css +347 -0
- data/web/bootstrap/css/bootstrap-theme.css.map +1 -0
- data/web/bootstrap/css/bootstrap-theme.min.css +7 -0
- data/web/bootstrap/css/bootstrap.css +4764 -4603
- data/web/bootstrap/css/bootstrap.css.map +1 -0
- data/web/bootstrap/css/bootstrap.min.css +6 -8
- data/web/bootstrap/fonts/glyphicons-halflings-regular.eot +0 -0
- data/web/bootstrap/fonts/glyphicons-halflings-regular.svg +229 -0
- data/web/bootstrap/fonts/glyphicons-halflings-regular.ttf +0 -0
- data/web/bootstrap/fonts/glyphicons-halflings-regular.woff +0 -0
- data/web/bootstrap/js/bootstrap.js +1372 -1448
- data/web/bootstrap/js/bootstrap.min.js +5 -5
- data/web/cli.html +14 -28
- data/web/index.html +15 -33
- data/web/ontologies.html +1089 -945
- data/web/webservices.html +12 -14
- metadata +24 -27
- data/lib/biointerchange/gff3o.rb +0 -525
- data/lib/biointerchange/gvf1o.rb +0 -1354
- data/web/bootstrap/css/bootstrap-responsive.css +0 -1040
- data/web/bootstrap/css/bootstrap-responsive.min.css +0 -9
- data/web/bootstrap/img/glyphicons-halflings-white.png +0 -0
- data/web/bootstrap/img/glyphicons-halflings.png +0 -0
@@ -8,7 +8,7 @@ class GFF3Reader < BioInterchange::Reader
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BioInterchange::Registry.register_reader(
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'biointerchange.gff3',
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GFF3Reader,
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-
[ 'name', 'name_uri', 'date' ],
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+
[ 'name', 'name_uri', 'date', 'batch_size' ],
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true,
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'Generic Feature Format Version 3 (GFF3) reader',
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[
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@@ -75,11 +75,15 @@ protected
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fasta_id = nil
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fasta_comment = nil
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fasta_sequence = nil
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@comments = [] # TODO Add comments to feature objects; add 'before' in serialization.
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begin
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line = gff3.readline
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line.chomp!
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-
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if line.start_with?('#') and not line.start_with?('##') then
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add_comment(@feature_set, line[1..-1].strip)
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next
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end
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if line.start_with?('##FASTA') then
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fasta_block = true
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end
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unless line.start_with?('##') then
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-
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begin
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add_feature(@feature_set, line)
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rescue ArgumentError => e
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# Potentially a string encoding issue (input not UTF-8). Try ISO-8859-1 and retry:
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add_feature(@feature_set, line.force_encoding('ISO-8859-1'))
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end
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feature_no += 1
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if @batch_size and feature_no >= @batch_size then
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@@ -165,6 +174,10 @@ protected
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feature_set.add(BioInterchange::Genomics::GFF3Feature.new(seqid, source, type, start_coordinate, end_coordinate, score, strand, phase, attributes))
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end
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def add_comment(feature_set, comment)
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@comments << comment
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end
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def add_pragma(feature_set, line)
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line.chomp!
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name, value = line[2..-1].split(/\s/, 2)
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@@ -0,0 +1,46 @@
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module BioInterchange::Genomics
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# Represents a single genomic feature of a VCF file.
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class VCFFeature < GFF3Feature
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# Creates a new feature representation. A feature is described on one line of the VCF file.
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#
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# +chromosome+:: an identifier that determines the chromosome on which the feature resides
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# +position+:: the feature locus on the chromosome
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# +id+:: a unique identifier of the feature
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# +reference_bases+:: reference alleles of the feature
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# +alternative_alleles+:: alternative alleles of the feature (non-reference alleles)
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# +quality_score+:: phred-scaled quality score for the assertions concerning reference-/alternative-alleles
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# +filters+:: list of VCF filters that a feature has failed
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# +info+:: a map of additional attributes associated with the feature
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# +samples+:: sample information specific to the described feature
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def initialize(chromosome, position, id, reference_bases, alternative_alleles, quality_score, filters, info = {}, samples = [])
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# Fill in phase, which is always omitted in GVF features (after 'strand', before 'attributes'):
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# Translations to somewhat fit the existing GFF3/GVF model (GFF3/GVF left, VCF right):
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#
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# sequence_id -> chromosome
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# source -> nil
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# type -> nil
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# start_coordinate -> position
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# end_coordinate -> position
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# score -> quality_score
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# strand -> nil
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# phase -> nil
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# attributes -> info
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#
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# Parameters that do not map directly to super's parameters are placed in `info`
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# with a space as prefix. For example, `reference_bases` becomes the key
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# ` reference_bases` in `info`.
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info[' id'] = [ id ] if id
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info[' reference_bases'] = [ reference_bases ]
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info[' alternative_alleles'] = alternative_alleles
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info[' filters'] = filters
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info[' samples'] = samples
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super(chromosome, nil, nil, position, position, quality_score, BioInterchange::Genomics::GFF3Feature::POSITIVE, nil, info)
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end
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end
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end
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@@ -0,0 +1,14 @@
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module BioInterchange::Genomics
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# A VCF feature set, which encapsules information of a single VCF file.
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class VCFFeatureSet < GFF3FeatureSet
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def uri
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super.sub(/^biointerchange:\/\/gff3\//, 'biointerchange://vcf/')
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end
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end
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end
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module BioInterchange::Genomics
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require 'date'
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class VCFReader < GFF3Reader
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# Register reader:
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BioInterchange::Registry.register_reader(
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'biointerchange.vcf',
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VCFReader,
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[ 'name', 'name_uri', 'date', 'batch_size' ],
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true,
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'Variant Call Format (VCF) version 4.1/4.2 reader',
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[
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[ 'date <date>', 'date when the GVF file was created (optional)' ],
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[ 'name <name>', 'name of the GVF file creator (optional)' ],
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[ 'name_id <id>', 'email address of the GVF file creator (optional)' ]
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]
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)
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# Creates a new instance of a Genome Variation Format (GVF) reader.
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#
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# +name+:: Optional name of the person who generated the GVF file.
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# +name_uri+:: Optional e-mail address of the person who generated the GVF file.
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# +date+:: Optional date of when the GVF file was produced.
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def initialize(name = nil, name_uri = nil, date = nil, batch_size = nil)
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# Remember: calling super without brackets passes all arguments of initialize!
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super
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end
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protected
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def create_feature_set
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BioInterchange::Genomics::VCFFeatureSet.new()
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end
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def add_pragma(feature_set, line)
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line.chomp!
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name, value = line[2..-1].split(/=/, 2)
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value.strip!
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# Interpret pragmas, and if not known, delegate to GFF3Reader (in alphabetical order):
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if name == 'assembly' then
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# attributes = split_attributes(value)
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# structured_attributes = feature_set.pragma(name)
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# structured_attributes = { name => [] } unless structured_attributes
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# structured_attributes[name] << attributes
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# feature_set.set_pragma(name, structured_attributes)
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elsif name == 'center' then
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#
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elsif name == 'contig' then
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self.add_vcf_pragma(feature_set, name, value)
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elsif name == 'fileDate' then
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feature_set.set_pragma(name, { name => Date.parse(value) })
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elsif name == 'fileformat' then
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feature_set.set_pragma(name, { name => value.sub(/^VCFv/, '').to_f })
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elsif name == 'FILTER' then
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self.add_vcf_pragma(feature_set, name, value)
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elsif name == 'FORMAT' then
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self.add_vcf_pragma(feature_set, name, value)
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elsif name == 'geneAnno' then
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#
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elsif name == 'ID' then
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#
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elsif name == 'INFO' then
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feature_set.set_pragma(name, vcf_mapping(value))
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elsif name == 'Number' then
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#
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elsif name == 'PEDIGREE' then
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self.add_vcf_pragma(feature_set, name, value)
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elsif name == 'phasing' then
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#
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elsif name == 'reference' then
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#
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elsif name == 'SAMPLE' then
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#
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elsif name == 'tcgaversion' then
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#
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elsif name == 'Type' then
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#
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elsif name == 'vcfProcessLog' then
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#
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elsif name == 'reference' then
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# 'reference' is not specified in VCF 4.1, but used in examples and real-world
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# VCF files nevertheless.
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# TODO What if reference already set?
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feature_set.set_pragma(name, value)
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else
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# Cannot be passed to super class, because GFF3 has inherently different pragma statements.
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feature_set.set_pragma(name, { name => value })
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end
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end
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# Adds pragma information where the pragma can appear multiple times
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# in the input (application: VCF). Each pragma information is still a hash,
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# which is stored in an array.
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#
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# +feature_set+:: feature set to which the pragma information is added
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# +name+:: name of the pragma under which the information is being stored
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# +value+:: hashmap of the actual pragma information (will be passed through vcf_mapping call)
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def add_vcf_pragma(feature_set, name, value)
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values = feature_set.pragma(name)
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if values then
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values << vcf_mapping(value)
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else
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values = [ vcf_mapping(value) ]
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end
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feature_set.set_pragma(name, values)
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end
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# Adds a comment to the feature set; ignores the header line that preceds VCF features.
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# Comments are added on a line-by-line basis.
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#
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# +feature_set+:: VCF feature set to which the comment line is being added
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# +comment+:: comment line in the VCF file
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def add_comment(feature_set, comment)
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if comment.start_with?("CHROM\tPOS\tID\tREF\tALT") then
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columns = comment.split("\t")
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@samples = columns[9..-1]
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@samples = [] unless @samples
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else
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@comment << comment
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end
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end
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# Adds a VCF feature to a VCF feature set.
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#
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# +feature_set+:: feature set to which the feature should be added to
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# +line+:: line from the VCF that describes the feature
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def add_feature(feature_set, line)
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line.chomp!
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chrom, pos, id, ref, alt, qual, filter, info, format, samples = line.split("\t")
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# Replace an unknown ID by nil, so that feature coordinates are used during serialization:
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id = nil
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+
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#
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# Split composite fields
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#
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# Alternative alleles:
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alt = alt.split(',')
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# Filters:
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filter = filter.split(';')
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# Feature information:
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info = info.split(';')
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info = info.map { |key_value_pair| key, values = key_value_pair.split('=', 2) }
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info = Hash[info]
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info = Hash[info.map { |key, value|
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if value then
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[ key, value.split(',') ]
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else
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[ key, true ]
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end
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}]
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# Format for following sample columns:
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format = format.split(':')
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# Sample columns (need to be further split in the writer -- depends on format):
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samples = samples.split("\t").map { |value|
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# Dot: not data provided for the sample
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if value == '.' then
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{}
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else
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values = value.split(':')
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Hash[format.zip(values)]
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end
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}
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feature_set.add(BioInterchange::Genomics::VCFFeature.new(chrom, pos, id, ref, alt, qual, filter, info, samples))
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end
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private
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# Takes a VCF meta-information string and returns a key-value mapping.
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#
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# +value+:: value of a meta-information assignment in VCF (key/value mappings of the form "<ID=value,...>")
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def vcf_mapping(value)
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value = value[1..-2]
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mapping = {}
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identifier = ''
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assignment = ''
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state = :id
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value.each_char { |character|
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if state == :value then
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if character == '"' then
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state = :quoted
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next
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else
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state = :plain
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end
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end
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+
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198
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state = :separator if state == :plain and character == ','
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+
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if state == :id then
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if character == '=' then
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state = :value
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assignment = ''
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else
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identifier << character
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end
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elsif state == :separator then
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if character == ',' then
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state = :id
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mapping[identifier] = assignment
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identifier = ''
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else
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# TODO Format error.
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end
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+
elsif state == :quoted then
|
216
|
+
if character == '"' then
|
217
|
+
state = :separator
|
218
|
+
mapping[identifier] = assignment
|
219
|
+
identifier = ''
|
220
|
+
else
|
221
|
+
assignment << character
|
222
|
+
end
|
223
|
+
elsif state == :plain then
|
224
|
+
assignment << character
|
225
|
+
else
|
226
|
+
# TODO Whoops. Report error.
|
227
|
+
end
|
228
|
+
}
|
229
|
+
|
230
|
+
mapping[identifier] = assignment unless identifier.empty?
|
231
|
+
|
232
|
+
mapping
|
233
|
+
end
|
234
|
+
|
235
|
+
end
|
236
|
+
|
237
|
+
end
|
238
|
+
|
data/lib/biointerchange/gfvo.rb
CHANGED
@@ -3,776 +3,873 @@ module BioInterchange
|
|
3
3
|
|
4
4
|
class GFVO
|
5
5
|
|
6
|
-
#
|
7
|
-
# (http://www.biointerchange.org/gfvo#
|
8
|
-
def self.
|
9
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
6
|
+
# Links to an entity for which supportive information is being provided.
|
7
|
+
# (http://www.biointerchange.org/gfvo#describes)
|
8
|
+
def self.describes
|
9
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#describes')
|
10
10
|
end
|
11
11
|
|
12
|
-
#
|
13
|
-
# (http://www.biointerchange.org/gfvo#
|
14
|
-
def self.
|
15
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
12
|
+
# Links to additional annotations about an entity.
|
13
|
+
# (http://www.biointerchange.org/gfvo#hasAnnotation)
|
14
|
+
def self.has_annotation
|
15
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#hasAnnotation')
|
16
16
|
end
|
17
17
|
|
18
|
-
#
|
19
|
-
# (http://www.biointerchange.org/gfvo#
|
20
|
-
def self.
|
21
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
18
|
+
# Links out to aggregate information for an entity.
|
19
|
+
# (http://www.biointerchange.org/gfvo#hasAttribute)
|
20
|
+
def self.has_attribute
|
21
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#hasAttribute')
|
22
22
|
end
|
23
23
|
|
24
|
-
#
|
25
|
-
# (http://www.biointerchange.org/gfvo#
|
26
|
-
def self.
|
27
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
24
|
+
# References an entity or resource that provides supporting/refuting evidence.
|
25
|
+
# (http://www.biointerchange.org/gfvo#hasEvidence)
|
26
|
+
def self.has_evidence
|
27
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#hasEvidence')
|
28
28
|
end
|
29
29
|
|
30
|
-
# Denotes
|
31
|
-
# (http://www.biointerchange.org/gfvo#
|
32
|
-
def self.
|
33
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
30
|
+
# Denotes the first entity of an ordered part relationship.
|
31
|
+
# (http://www.biointerchange.org/gfvo#hasFirstPart)
|
32
|
+
def self.has_first_part
|
33
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#hasFirstPart')
|
34
34
|
end
|
35
35
|
|
36
|
-
#
|
37
|
-
# (http://www.biointerchange.org/gfvo#
|
38
|
-
def self.
|
39
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
36
|
+
# Links out to an identifier.
|
37
|
+
# (http://www.biointerchange.org/gfvo#hasIdentifier)
|
38
|
+
def self.has_identifier
|
39
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#hasIdentifier')
|
40
40
|
end
|
41
41
|
|
42
|
-
#
|
43
|
-
# (http://www.biointerchange.org/gfvo#
|
44
|
-
def self.
|
45
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
42
|
+
# Links out to an entity that is the input of a "Process" subclass.
|
43
|
+
# (http://www.biointerchange.org/gfvo#hasInput)
|
44
|
+
def self.has_input
|
45
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#hasInput')
|
46
46
|
end
|
47
47
|
|
48
|
-
#
|
49
|
-
# (http://www.biointerchange.org/gfvo#
|
50
|
-
def self.
|
51
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
48
|
+
# Denotes the last entity of an ordered part relationship.
|
49
|
+
# (http://www.biointerchange.org/gfvo#hasLastPart)
|
50
|
+
def self.has_last_part
|
51
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#hasLastPart')
|
52
52
|
end
|
53
53
|
|
54
|
-
# Denotes
|
55
|
-
# (http://www.biointerchange.org/gfvo#
|
56
|
-
def self.
|
57
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
54
|
+
# Denotes membership for "Collection", "Catalog" and "File" instances.
|
55
|
+
# (http://www.biointerchange.org/gfvo#hasMember)
|
56
|
+
def self.has_member
|
57
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#hasMember')
|
58
58
|
end
|
59
59
|
|
60
|
-
#
|
61
|
-
# (http://www.biointerchange.org/gfvo#
|
62
|
-
def self.
|
63
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
60
|
+
# Denotes a compositional relationship to other entities, where the ordering of the composition of entities carries meaning.
|
61
|
+
# (http://www.biointerchange.org/gfvo#hasOrderedPart)
|
62
|
+
def self.has_ordered_part
|
63
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#hasOrderedPart')
|
64
64
|
end
|
65
65
|
|
66
|
-
#
|
67
|
-
# (http://www.biointerchange.org/gfvo#
|
68
|
-
def self.
|
69
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
66
|
+
# Links out to an entity that is the output of a "Process" subclass.
|
67
|
+
# (http://www.biointerchange.org/gfvo#hasOutput)
|
68
|
+
def self.has_output
|
69
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#hasOutput')
|
70
70
|
end
|
71
71
|
|
72
|
-
#
|
73
|
-
# (http://www.biointerchange.org/gfvo#
|
74
|
-
def self.
|
75
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
72
|
+
# Denotes a compositional relationship to other entities.
|
73
|
+
# (http://www.biointerchange.org/gfvo#hasPart)
|
74
|
+
def self.has_part
|
75
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#hasPart')
|
76
76
|
end
|
77
77
|
|
78
|
-
#
|
79
|
-
# (http://www.biointerchange.org/gfvo#
|
80
|
-
def self.
|
81
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
78
|
+
# Denotes the participation of other entities in processes.
|
79
|
+
# (http://www.biointerchange.org/gfvo#hasParticipant)
|
80
|
+
def self.has_participant
|
81
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#hasParticipant')
|
82
82
|
end
|
83
83
|
|
84
|
-
#
|
85
|
-
# (http://www.biointerchange.org/gfvo#
|
86
|
-
def self.
|
87
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
84
|
+
# Links out to an entity that provides qualitative information.
|
85
|
+
# (http://www.biointerchange.org/gfvo#hasQuality)
|
86
|
+
def self.has_quality
|
87
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#hasQuality')
|
88
88
|
end
|
89
89
|
|
90
|
-
#
|
91
|
-
# (http://www.biointerchange.org/gfvo#
|
92
|
-
def self.
|
93
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
90
|
+
# Denotes information origin.
|
91
|
+
# (http://www.biointerchange.org/gfvo#hasSource)
|
92
|
+
def self.has_source
|
93
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#hasSource')
|
94
94
|
end
|
95
95
|
|
96
|
-
#
|
97
|
-
# (http://www.biointerchange.org/gfvo#
|
98
|
-
def self.
|
99
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
96
|
+
# References an entity about which information is provided for.
|
97
|
+
# (http://www.biointerchange.org/gfvo#isAbout)
|
98
|
+
def self.is_about
|
99
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#isAbout')
|
100
100
|
end
|
101
101
|
|
102
|
-
#
|
103
|
-
# (http://www.biointerchange.org/gfvo#
|
104
|
-
def self.
|
105
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
102
|
+
# Denotes that an entity is affected by another entity.
|
103
|
+
# (http://www.biointerchange.org/gfvo#isAffectedBy)
|
104
|
+
def self.is_affected_by
|
105
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#isAffectedBy')
|
106
106
|
end
|
107
107
|
|
108
|
-
#
|
109
|
-
# (http://www.biointerchange.org/gfvo#
|
110
|
-
def self.
|
111
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
108
|
+
# Denotes the trailing occurrence or succession of the subject in regards to the object.
|
109
|
+
# (http://www.biointerchange.org/gfvo#isAfter)
|
110
|
+
def self.is_after
|
111
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#isAfter')
|
112
112
|
end
|
113
113
|
|
114
|
-
#
|
115
|
-
# (http://www.biointerchange.org/gfvo#
|
116
|
-
def self.
|
117
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
114
|
+
# Denotes that an entity is an attribute of the entity that this property links out to.
|
115
|
+
# (http://www.biointerchange.org/gfvo#isAttributeOf)
|
116
|
+
def self.is_attribute_of
|
117
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#isAttributeOf')
|
118
118
|
end
|
119
119
|
|
120
|
-
#
|
121
|
-
# (http://www.biointerchange.org/gfvo#
|
122
|
-
def self.
|
123
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
120
|
+
# Denotes the leading occurrence or precedence of the subject in regards to the object.
|
121
|
+
# (http://www.biointerchange.org/gfvo#isBefore)
|
122
|
+
def self.is_before
|
123
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#isBefore')
|
124
124
|
end
|
125
125
|
|
126
|
-
#
|
127
|
-
# (http://www.biointerchange.org/gfvo#
|
128
|
-
def self.
|
129
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
126
|
+
# Denotes the process or method that created an entity.
|
127
|
+
# (http://www.biointerchange.org/gfvo#isCreatedBy)
|
128
|
+
def self.is_created_by
|
129
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#isCreatedBy')
|
130
130
|
end
|
131
131
|
|
132
|
-
#
|
133
|
-
# (http://www.biointerchange.org/gfvo#
|
134
|
-
def self.
|
135
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
132
|
+
# Provides a description of the subject via reference to an object that provides further information on the subject.
|
133
|
+
# (http://www.biointerchange.org/gfvo#isDescribedBy)
|
134
|
+
def self.is_described_by
|
135
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#isDescribedBy')
|
136
136
|
end
|
137
137
|
|
138
|
-
#
|
139
|
-
# (http://www.biointerchange.org/gfvo#
|
140
|
-
def self.
|
141
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
138
|
+
# Denotes the location of genomic feature on a landmark.
|
139
|
+
# (http://www.biointerchange.org/gfvo#isLocatedOn)
|
140
|
+
def self.is_located_on
|
141
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#isLocatedOn')
|
142
142
|
end
|
143
143
|
|
144
|
-
#
|
145
|
-
# (http://www.biointerchange.org/gfvo#
|
146
|
-
def self.
|
147
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
144
|
+
# Denotes that an entity is an intrinsic component of an encapsulating entity.
|
145
|
+
# (http://www.biointerchange.org/gfvo#isPartOf)
|
146
|
+
def self.is_part_of
|
147
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#isPartOf')
|
148
148
|
end
|
149
149
|
|
150
|
-
#
|
151
|
-
# (http://www.biointerchange.org/gfvo#
|
152
|
-
def self.
|
153
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
150
|
+
# Denotes participation with another entity.
|
151
|
+
# (http://www.biointerchange.org/gfvo#isParticipantIn)
|
152
|
+
def self.is_participant_in
|
153
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#isParticipantIn')
|
154
154
|
end
|
155
155
|
|
156
|
-
#
|
157
|
-
# (http://www.biointerchange.org/gfvo#
|
158
|
-
def self.
|
159
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
156
|
+
# References an entity or resource that provides refuting evidence.
|
157
|
+
# (http://www.biointerchange.org/gfvo#isRefutedBy)
|
158
|
+
def self.is_refuted_by
|
159
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#isRefutedBy')
|
160
160
|
end
|
161
161
|
|
162
|
-
#
|
163
|
-
# (http://www.biointerchange.org/gfvo#
|
164
|
-
def self.
|
165
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
162
|
+
# Denotes that an entity is the source of the entity that this property links out to.
|
163
|
+
# (http://www.biointerchange.org/gfvo#isSourceOf)
|
164
|
+
def self.is_source_of
|
165
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#isSourceOf')
|
166
166
|
end
|
167
167
|
|
168
|
-
#
|
169
|
-
# (http://www.biointerchange.org/gfvo#
|
170
|
-
def self.
|
171
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
168
|
+
# Denotes spatio-temporal relations to other entities.
|
169
|
+
# (http://www.biointerchange.org/gfvo#isSpatiotemporallyRelatedTo)
|
170
|
+
def self.is_spatiotemporally_related_to
|
171
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#isSpatiotemporallyRelatedTo')
|
172
172
|
end
|
173
173
|
|
174
|
-
#
|
175
|
-
# (http://www.biointerchange.org/gfvo#
|
176
|
-
def self.
|
177
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
174
|
+
# References an entity or resource that provides supporting evidence.
|
175
|
+
# (http://www.biointerchange.org/gfvo#isSupportedBy)
|
176
|
+
def self.is_supported_by
|
177
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#isSupportedBy')
|
178
178
|
end
|
179
179
|
|
180
|
-
#
|
181
|
-
#
|
182
|
-
|
183
|
-
|
180
|
+
# Denotes a temporarily constraint "isPartOf" relationship. The temporal restriction expresses that the relationship is not universally true.
|
181
|
+
#
|
182
|
+
# This property can be used to express "Derives_from" relations in GFF3.
|
183
|
+
# (http://www.biointerchange.org/gfvo#isTemporarilyPartOf)
|
184
|
+
def self.is_temporarily_part_of
|
185
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#isTemporarilyPartOf')
|
184
186
|
end
|
185
187
|
|
186
|
-
#
|
187
|
-
# (http://www.biointerchange.org/gfvo#
|
188
|
-
def self.
|
189
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
188
|
+
# References another entity or resource.
|
189
|
+
# (http://www.biointerchange.org/gfvo#references)
|
190
|
+
def self.references
|
191
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#references')
|
190
192
|
end
|
191
193
|
|
192
|
-
#
|
193
|
-
# (http://www.biointerchange.org/gfvo#
|
194
|
-
def self.
|
195
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
194
|
+
# References an entity, where additional information is provided to augment the reference.
|
195
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# 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.
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# Denoting sex of a female individual. A female is defined as an individual producing ova.
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# 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.
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# Details about the fragment-read (single-end read) sequencing technology used to gather the data in a set.
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# (http://www.biointerchange.org/gfvo#FragmentReadPlatform)
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def self.FragmentReadPlatform
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# A functional specification of bioinformatics data, i.e. the specification of genomic material that potentially has biological function.
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# (http://www.biointerchange.org/gfvo#FunctionalSpecification)
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def self.FunctionalSpecification
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return RDF::URI.new('http://www.biointerchange.org/gfvo#FunctionalSpecification')
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
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# 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.
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# (http://www.biointerchange.org/gfvo#GameticPhase)
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def self.GameticPhase
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return RDF::URI.new('http://www.biointerchange.org/gfvo#GameticPhase')
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def self.
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
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# Representation of a genome. Genomic features that constitute the genome may be linked via one or more "Collection", "Catalog", "Contig", "Scaffold" or "File" instances.
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# (http://www.biointerchange.org/gfvo#Genome)
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def self.Genome
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return RDF::URI.new('http://www.biointerchange.org/gfvo#Genome')
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def self.
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
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# A genome analysis denotes the type of procedure that was carried out to derive information from a genome assembly.
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# (http://www.biointerchange.org/gfvo#GenomeAnalysis)
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def self.GenomeAnalysis
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return RDF::URI.new('http://www.biointerchange.org/gfvo#GenomeAnalysis')
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def self.
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
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# Provides information about the source of the data.
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# (http://www.biointerchange.org/gfvo#GenomicAscertainingMethod)
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def self.GenomicAscertainingMethod
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return RDF::URI.new('http://www.biointerchange.org/gfvo#GenomicAscertainingMethod')
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# 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.
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#
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# 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.
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#
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# Example: "A/G" denotes a genotype with alleles "A" and "G".
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# (http://www.biointerchange.org/gfvo#Genotype)
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def self.Genotype
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return RDF::URI.new('http://www.biointerchange.org/gfvo#Genotype')
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
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# 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.
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# (http://www.biointerchange.org/gfvo#Genotyping)
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def self.Genotyping
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return RDF::URI.new('http://www.biointerchange.org/gfvo#Genotyping')
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#
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def self.
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
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# The germline feature class captures information about genomic sequence features arising from germline cells.
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# (http://www.biointerchange.org/gfvo#GermlineCell)
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def self.GermlineCell
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return RDF::URI.new('http://www.biointerchange.org/gfvo#GermlineCell')
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#
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# (http://www.biointerchange.org/gfvo#
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def self.
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
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# Helix structure denotes the physical shape of biopolymers.
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# (http://www.biointerchange.org/gfvo#HelixStructure)
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def self.HelixStructure
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return RDF::URI.new('http://www.biointerchange.org/gfvo#HelixStructure')
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#
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def self.
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
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# A sequence alteration with hemizygous alleles.
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# (http://www.biointerchange.org/gfvo#Hemizygous)
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def self.Hemizygous
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return RDF::URI.new('http://www.biointerchange.org/gfvo#Hemizygous')
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end
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#
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# (http://www.biointerchange.org/gfvo#
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def self.
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
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# 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.
|
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# (http://www.biointerchange.org/gfvo#Heritage)
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def self.Heritage
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return RDF::URI.new('http://www.biointerchange.org/gfvo#Heritage')
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end
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#
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# (http://www.biointerchange.org/gfvo#
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def self.
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
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# Denoting sex of an individual that contains both male and female gametes.
|
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# (http://www.biointerchange.org/gfvo#Hermaphrodite)
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def self.Hermaphrodite
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return RDF::URI.new('http://www.biointerchange.org/gfvo#Hermaphrodite')
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end
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# A
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# (http://www.biointerchange.org/gfvo#
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def self.
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
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# A sequence alteration with heterozygous alleles.
|
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# (http://www.biointerchange.org/gfvo#Heterozygous)
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def self.Heterozygous
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return RDF::URI.new('http://www.biointerchange.org/gfvo#Heterozygous')
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end
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# A
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# (http://www.biointerchange.org/gfvo#
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def self.
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
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# A sequence alteration with homozygous alleles.
|
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# (http://www.biointerchange.org/gfvo#Homozygous)
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def self.Homozygous
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return RDF::URI.new('http://www.biointerchange.org/gfvo#Homozygous')
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end
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#
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# (http://www.biointerchange.org/gfvo#
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def self.
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
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# 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.
|
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# (http://www.biointerchange.org/gfvo#Identifier)
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def self.Identifier
|
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return RDF::URI.new('http://www.biointerchange.org/gfvo#Identifier')
|
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end
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#
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# (http://www.biointerchange.org/gfvo#
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def self.
|
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
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# An information content entity requires background information or specific domain knowledge to be interpreted correctly.
|
491
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# (http://www.biointerchange.org/gfvo#InformationContentEntity)
|
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+
def self.InformationContentEntity
|
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return RDF::URI.new('http://www.biointerchange.org/gfvo#InformationContentEntity')
|
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end
|
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#
|
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# (http://www.biointerchange.org/gfvo#
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def self.
|
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
496
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+
# Describing interaction between features, such as the effect of a feature variant on another feature.
|
497
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+
# (http://www.biointerchange.org/gfvo#Interaction)
|
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+
def self.Interaction
|
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return RDF::URI.new('http://www.biointerchange.org/gfvo#Interaction')
|
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end
|
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# A
|
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# (http://www.biointerchange.org/gfvo#
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def self.
|
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
502
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# 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.
|
503
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+
# (http://www.biointerchange.org/gfvo#Label)
|
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def self.Label
|
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return RDF::URI.new('http://www.biointerchange.org/gfvo#Label')
|
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end
|
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|
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#
|
499
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# (http://www.biointerchange.org/gfvo#
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500
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def self.
|
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
508
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+
# 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.
|
509
|
+
# (http://www.biointerchange.org/gfvo#Landmark)
|
510
|
+
def self.Landmark
|
511
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Landmark')
|
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end
|
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#
|
505
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# (http://www.biointerchange.org/gfvo#
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def self.
|
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
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# Likelihood is the hypothetical probability of the occurrence of a certain event.
|
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# (http://www.biointerchange.org/gfvo#Likelihood)
|
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def self.Likelihood
|
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return RDF::URI.new('http://www.biointerchange.org/gfvo#Likelihood')
|
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end
|
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|
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#
|
511
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-
# (http://www.biointerchange.org/gfvo#
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def self.
|
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
520
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# A locus refers to a position (possibly multi-dimensional) within a genome or proteome.
|
521
|
+
# (http://www.biointerchange.org/gfvo#Locus)
|
522
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def self.Locus
|
523
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return RDF::URI.new('http://www.biointerchange.org/gfvo#Locus')
|
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end
|
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# A
|
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# (http://www.biointerchange.org/gfvo#
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def self.
|
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|
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return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
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# Denoting sex of a male individual. A male is defined as an individual producing spermatozoa.
|
527
|
+
# (http://www.biointerchange.org/gfvo#Male)
|
528
|
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def self.Male
|
529
|
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return RDF::URI.new('http://www.biointerchange.org/gfvo#Male')
|
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530
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end
|
521
531
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|
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#
|
523
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# (http://www.biointerchange.org/gfvo#
|
524
|
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def self.
|
525
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
532
|
+
# Denotes a match between the reference sequence and target sequence.
|
533
|
+
# (http://www.biointerchange.org/gfvo#Match)
|
534
|
+
def self.Match
|
535
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Match')
|
526
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|
end
|
527
537
|
|
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# A
|
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# (http://www.biointerchange.org/gfvo#
|
530
|
-
def self.
|
531
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
538
|
+
# A material entity represents a physical object. In the context of genomic features and variations, material entities are cells, organisms, sequences, chromosomes, etc.
|
539
|
+
# (http://www.biointerchange.org/gfvo#MaterialEntity)
|
540
|
+
def self.MaterialEntity
|
541
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#MaterialEntity')
|
532
542
|
end
|
533
543
|
|
534
|
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#
|
535
|
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# (http://www.biointerchange.org/gfvo#
|
536
|
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def self.
|
537
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
544
|
+
# Maternal heritage is the passing of traits from a female to her ancestors.
|
545
|
+
# (http://www.biointerchange.org/gfvo#MaternalHeritage)
|
546
|
+
def self.MaternalHeritage
|
547
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#MaternalHeritage')
|
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548
|
end
|
539
549
|
|
540
|
-
#
|
541
|
-
# (http://www.biointerchange.org/gfvo#
|
542
|
-
def self.
|
543
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
550
|
+
# Insertion or deletion of a mobile element. The exact modification is determined by a type of the Variation Ontology.
|
551
|
+
# (http://www.biointerchange.org/gfvo#MobileElementSequenceVariant)
|
552
|
+
def self.MobileElementSequenceVariant
|
553
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#MobileElementSequenceVariant')
|
554
|
+
end
|
555
|
+
|
556
|
+
# A name assigns an entity a non-formal term (or multiples thereof) that can provide information about the entities identity.
|
557
|
+
# (http://www.biointerchange.org/gfvo#Name)
|
558
|
+
def self.Name
|
559
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Name')
|
560
|
+
end
|
561
|
+
|
562
|
+
# A note is a short textual description.
|
563
|
+
# (http://www.biointerchange.org/gfvo#Note)
|
564
|
+
def self.Note
|
565
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Note')
|
544
566
|
end
|
545
567
|
|
546
|
-
#
|
547
|
-
# (http://www.biointerchange.org/gfvo#
|
548
|
-
def self.
|
549
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
568
|
+
# Number of reads supporting a particular feature or variant.
|
569
|
+
# (http://www.biointerchange.org/gfvo#NumberOfReads)
|
570
|
+
def self.Number_ofReads
|
571
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#NumberOfReads')
|
550
572
|
end
|
551
573
|
|
552
|
-
#
|
553
|
-
# (http://www.biointerchange.org/gfvo#
|
554
|
-
def self.
|
555
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
574
|
+
# 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.
|
575
|
+
# (http://www.biointerchange.org/gfvo#Object)
|
576
|
+
def self.Object
|
577
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Object')
|
556
578
|
end
|
557
579
|
|
558
580
|
# Details about the paired-end read sequencing technology used to gather the data in a set.
|
559
581
|
# (http://www.biointerchange.org/gfvo#PairedEndReadPlatform)
|
560
|
-
def self.
|
582
|
+
def self.PairedEndReadPlatform
|
561
583
|
return RDF::URI.new('http://www.biointerchange.org/gfvo#PairedEndReadPlatform')
|
562
584
|
end
|
563
585
|
|
564
|
-
#
|
565
|
-
# (http://www.biointerchange.org/gfvo#
|
566
|
-
def self.
|
567
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
586
|
+
# Paternal heritage is the passing of traits from a male to his ancestors.
|
587
|
+
# (http://www.biointerchange.org/gfvo#PaternalHeritage)
|
588
|
+
def self.PaternalHeritage
|
589
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#PaternalHeritage')
|
568
590
|
end
|
569
591
|
|
570
|
-
# A
|
571
|
-
# (http://www.biointerchange.org/gfvo#
|
572
|
-
def self.
|
573
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
592
|
+
# 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.
|
593
|
+
# (http://www.biointerchange.org/gfvo#PeptideSequence)
|
594
|
+
def self.PeptideSequence
|
595
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#PeptideSequence')
|
596
|
+
end
|
597
|
+
|
598
|
+
# A phenotype description represents additional information about a sequenced individual's phenotype. A sequenced individual is represented by instances of the "Sequenced Individual" class.
|
599
|
+
# (http://www.biointerchange.org/gfvo#Phenotype)
|
600
|
+
def self.Phenotype
|
601
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Phenotype')
|
602
|
+
end
|
603
|
+
|
604
|
+
# The Phred score can be used to assign quality scores to base calls of DNA sequences.
|
605
|
+
# (http://www.biointerchange.org/gfvo#PhredScore)
|
606
|
+
def self.PhredScore
|
607
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#PhredScore')
|
574
608
|
end
|
575
609
|
|
576
610
|
# 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, http://loinc.org), do not define the meaning or intended usage of the term "prenatal" either.
|
577
|
-
# (http://www.biointerchange.org/gfvo#
|
578
|
-
def self.
|
579
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
611
|
+
# (http://www.biointerchange.org/gfvo#PrenatalCell)
|
612
|
+
def self.PrenatalCell
|
613
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#PrenatalCell')
|
614
|
+
end
|
615
|
+
|
616
|
+
# 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.
|
617
|
+
# (http://www.biointerchange.org/gfvo#Process)
|
618
|
+
def self.Process
|
619
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Process')
|
620
|
+
end
|
621
|
+
|
622
|
+
# A protein sequence is a peptide sequence which represents the primary structure of a protein.
|
623
|
+
# (http://www.biointerchange.org/gfvo#ProteinSequence)
|
624
|
+
def self.ProteinSequence
|
625
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#ProteinSequence')
|
580
626
|
end
|
581
627
|
|
582
|
-
#
|
583
|
-
# (http://www.biointerchange.org/gfvo#
|
584
|
-
def self.
|
585
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
628
|
+
# 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").
|
629
|
+
# (http://www.biointerchange.org/gfvo#Quality)
|
630
|
+
def self.Quality
|
631
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Quality')
|
632
|
+
end
|
633
|
+
|
634
|
+
# 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.
|
635
|
+
# (http://www.biointerchange.org/gfvo#Quantity)
|
636
|
+
def self.Quantity
|
637
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Quantity')
|
638
|
+
end
|
639
|
+
|
640
|
+
# Information about features and variants is based on RNA sequencing.
|
641
|
+
# (http://www.biointerchange.org/gfvo#RNASequencing)
|
642
|
+
def self.RNASequencing
|
643
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#RNASequencing')
|
586
644
|
end
|
587
645
|
|
588
646
|
# 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.
|
589
|
-
# (http://www.biointerchange.org/gfvo#
|
590
|
-
def self.
|
591
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
647
|
+
# (http://www.biointerchange.org/gfvo#ReferenceSequence)
|
648
|
+
def self.ReferenceSequence
|
649
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#ReferenceSequence')
|
592
650
|
end
|
593
651
|
|
594
|
-
# Denotes a gap in the reference sequence for an alignment.
|
652
|
+
# Denotes a gap in the reference sequence for an alignment.
|
595
653
|
# (http://www.biointerchange.org/gfvo#ReferenceSequenceGap)
|
596
|
-
def self.
|
654
|
+
def self.ReferenceSequenceGap
|
597
655
|
return RDF::URI.new('http://www.biointerchange.org/gfvo#ReferenceSequenceGap')
|
598
656
|
end
|
599
657
|
|
600
|
-
# Denotes a frameshift backwards (reverse) in the reference sequence.
|
658
|
+
# Denotes a frameshift backwards (reverse) in the reference sequence.
|
601
659
|
# (http://www.biointerchange.org/gfvo#ReverseReferenceSequenceFrameshift)
|
602
|
-
def self.
|
660
|
+
def self.ReverseReferenceSequenceFrameshift
|
603
661
|
return RDF::URI.new('http://www.biointerchange.org/gfvo#ReverseReferenceSequenceFrameshift')
|
604
662
|
end
|
605
663
|
|
606
|
-
# A
|
607
|
-
# (http://www.biointerchange.org/gfvo#
|
608
|
-
def self.
|
609
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
664
|
+
# 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.
|
665
|
+
# (http://www.biointerchange.org/gfvo#Sample)
|
666
|
+
def self.Sample
|
667
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Sample')
|
668
|
+
end
|
669
|
+
|
670
|
+
# A scaffold is the aggregation of multiple contigs to form a larger continuous sequencing region.
|
671
|
+
# (http://www.biointerchange.org/gfvo#Scaffold)
|
672
|
+
def self.Scaffold
|
673
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Scaffold')
|
610
674
|
end
|
611
675
|
|
612
|
-
#
|
613
|
-
# (http://www.biointerchange.org/gfvo#
|
614
|
-
def self.
|
615
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
676
|
+
# A measure that permits the ranking of entities.
|
677
|
+
# (http://www.biointerchange.org/gfvo#Score)
|
678
|
+
def self.Score
|
679
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Score')
|
616
680
|
end
|
617
681
|
|
618
|
-
#
|
619
|
-
# (http://www.biointerchange.org/gfvo#
|
620
|
-
def self.
|
621
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
682
|
+
# 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.
|
683
|
+
# (http://www.biointerchange.org/gfvo#Sequence)
|
684
|
+
def self.Sequence
|
685
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Sequence')
|
622
686
|
end
|
623
687
|
|
624
|
-
#
|
688
|
+
# A sequence alignment denotes the congruence of two sequences.
|
689
|
+
# In GFF3, a sequence alignment can be a nucleotide-to-nucleotide or protein-to-nucleotide alignment (see "The Gap Attribute", http://sequenceontology.org/resources/gff3.html). "Alignment Operation" class instances denote the actual steps that the constitute the sequence alignment.
|
690
|
+
# (http://www.biointerchange.org/gfvo#SequenceAlignment)
|
691
|
+
def self.SequenceAlignment
|
692
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#SequenceAlignment')
|
693
|
+
end
|
694
|
+
|
695
|
+
# 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.
|
696
|
+
# (http://www.biointerchange.org/gfvo#SequenceAlignmentOperation)
|
697
|
+
def self.SequenceAlignmentOperation
|
698
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#SequenceAlignmentOperation')
|
699
|
+
end
|
700
|
+
|
701
|
+
# 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.
|
702
|
+
# (http://www.biointerchange.org/gfvo#SequenceVariant)
|
703
|
+
def self.SequenceVariant
|
704
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#SequenceVariant')
|
705
|
+
end
|
706
|
+
|
707
|
+
# Aggregated sequencing information for a particular individual.
|
625
708
|
# (http://www.biointerchange.org/gfvo#SequencedIndividual)
|
626
|
-
def self.
|
709
|
+
def self.SequencedIndividual
|
627
710
|
return RDF::URI.new('http://www.biointerchange.org/gfvo#SequencedIndividual')
|
628
711
|
end
|
629
712
|
|
630
|
-
#
|
631
|
-
# (http://www.biointerchange.org/gfvo#
|
632
|
-
def self.
|
633
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
713
|
+
# Details about the sequencing/microarray technology used to gather the data in a set.
|
714
|
+
# (http://www.biointerchange.org/gfvo#SequencingTechnologyPlatform)
|
715
|
+
def self.SequencingTechnologyPlatform
|
716
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#SequencingTechnologyPlatform')
|
634
717
|
end
|
635
718
|
|
636
|
-
#
|
637
|
-
# (http://www.biointerchange.org/gfvo#
|
638
|
-
def self.
|
639
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
719
|
+
# Biological sex of an individual.
|
720
|
+
# (http://www.biointerchange.org/gfvo#Sex)
|
721
|
+
def self.Sex
|
722
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Sex')
|
640
723
|
end
|
641
724
|
|
642
725
|
# The somatic feature class captures information about genomic sequence features arising from somatic cells.
|
643
|
-
# (http://www.biointerchange.org/gfvo#
|
644
|
-
def self.
|
645
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
646
|
-
end
|
647
|
-
|
648
|
-
# A structured attribute denotes a tag/value pair where the value is a composite, but which is not defined in the GVF specification. The GVF specification does not explicitly permit user-defined structured attributes (see "Structured Pragmas" in http://sequenceontology.org/resources/gvf.html), but it is conceivable that an RDFization tool might support this use case. For some loosly defined structured data in GVF, the "Structured Attribute" class is used as well to capture the non-exhaustive list of possible data assignments of the GVF specification.
|
649
|
-
# (http://www.biointerchange.org/gfvo#StructuredAttribute)
|
650
|
-
def self.Structured_Attribute
|
651
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#StructuredAttribute')
|
726
|
+
# (http://www.biointerchange.org/gfvo#SomaticCell)
|
727
|
+
def self.SomaticCell
|
728
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#SomaticCell')
|
652
729
|
end
|
653
730
|
|
654
|
-
# A
|
655
|
-
# (http://www.biointerchange.org/gfvo#
|
656
|
-
def self.
|
657
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
731
|
+
# 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.
|
732
|
+
# (http://www.biointerchange.org/gfvo#Span)
|
733
|
+
def self.Span
|
734
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Span')
|
658
735
|
end
|
659
736
|
|
660
|
-
# Denotes a gap in the target sequence for an alignment.
|
737
|
+
# Denotes a gap in the target sequence for an alignment.
|
661
738
|
# (http://www.biointerchange.org/gfvo#TargetSequenceGap)
|
662
|
-
def self.
|
739
|
+
def self.TargetSequenceGap
|
663
740
|
return RDF::URI.new('http://www.biointerchange.org/gfvo#TargetSequenceGap')
|
664
741
|
end
|
665
742
|
|
666
|
-
#
|
667
|
-
# (http://www.biointerchange.org/gfvo#
|
668
|
-
def self.
|
669
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
743
|
+
# Total number of reads covering a feature or variant.
|
744
|
+
# (http://www.biointerchange.org/gfvo#TotalNumberOfReads)
|
745
|
+
def self.TotalNumber_ofReads
|
746
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#TotalNumberOfReads')
|
670
747
|
end
|
671
748
|
|
672
|
-
#
|
673
|
-
# (http://www.biointerchange.org/gfvo#
|
674
|
-
def self.
|
675
|
-
return RDF::URI.new('http://www.biointerchange.org/gfvo#
|
749
|
+
# Denotes the technique of calling genomic feature variants in a genome assembly.
|
750
|
+
# (http://www.biointerchange.org/gfvo#VariantCalling)
|
751
|
+
def self.VariantCalling
|
752
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#VariantCalling')
|
753
|
+
end
|
754
|
+
|
755
|
+
# A version names a release of a software, dataset, or other resource. A versioned resource is not necessarily public.
|
756
|
+
# (http://www.biointerchange.org/gfvo#Version)
|
757
|
+
def self.Version
|
758
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Version')
|
759
|
+
end
|
760
|
+
|
761
|
+
# Helical structure as first proposed by Watson and Crick.
|
762
|
+
#
|
763
|
+
# Can be used to indicate a false "Is_circular" attribute in GFF3 and GVF.
|
764
|
+
# (http://www.biointerchange.org/gfvo#WatsonCrickHelix)
|
765
|
+
def self.WatsonCrickHelix
|
766
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#WatsonCrickHelix')
|
767
|
+
end
|
768
|
+
|
769
|
+
# Zygosity denotes the similarities of a specific allele in the genome of an organism.
|
770
|
+
# (http://www.biointerchange.org/gfvo#Zygosity)
|
771
|
+
def self.Zygosity
|
772
|
+
return RDF::URI.new('http://www.biointerchange.org/gfvo#Zygosity')
|
676
773
|
end
|
677
774
|
|
678
775
|
# Determines whether the given URI is an object property.
|
679
776
|
#
|
680
777
|
# +uri+:: URI that is tested for being an object property
|
681
778
|
def self.is_object_property?(uri)
|
682
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
779
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#describes') then
|
683
780
|
return true
|
684
781
|
end
|
685
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
782
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasAnnotation') then
|
686
783
|
return true
|
687
784
|
end
|
688
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
785
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasAttribute') then
|
689
786
|
return true
|
690
787
|
end
|
691
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
788
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasEvidence') then
|
692
789
|
return true
|
693
790
|
end
|
694
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
791
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasFirstPart') then
|
695
792
|
return true
|
696
793
|
end
|
697
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
794
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasIdentifier') then
|
698
795
|
return true
|
699
796
|
end
|
700
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
797
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasInput') then
|
701
798
|
return true
|
702
799
|
end
|
703
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
800
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasLastPart') then
|
704
801
|
return true
|
705
802
|
end
|
706
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
803
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasMember') then
|
707
804
|
return true
|
708
805
|
end
|
709
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
806
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasOrderedPart') then
|
710
807
|
return true
|
711
808
|
end
|
712
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
809
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasOutput') then
|
713
810
|
return true
|
714
811
|
end
|
715
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
812
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasPart') then
|
716
813
|
return true
|
717
814
|
end
|
718
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
815
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasParticipant') then
|
719
816
|
return true
|
720
817
|
end
|
721
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
818
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasQuality') then
|
722
819
|
return true
|
723
820
|
end
|
724
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
821
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasSource') then
|
725
822
|
return true
|
726
823
|
end
|
727
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
824
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isAbout') then
|
728
825
|
return true
|
729
826
|
end
|
730
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
827
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isAffectedBy') then
|
731
828
|
return true
|
732
829
|
end
|
733
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
830
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isAfter') then
|
734
831
|
return true
|
735
832
|
end
|
736
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
833
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isAttributeOf') then
|
737
834
|
return true
|
738
835
|
end
|
739
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
836
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isBefore') then
|
740
837
|
return true
|
741
838
|
end
|
742
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
839
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isCreatedBy') then
|
743
840
|
return true
|
744
841
|
end
|
745
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
842
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isDescribedBy') then
|
746
843
|
return true
|
747
844
|
end
|
748
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
845
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isLocatedOn') then
|
749
846
|
return true
|
750
847
|
end
|
751
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
848
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isPartOf') then
|
752
849
|
return true
|
753
850
|
end
|
754
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
851
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isParticipantIn') then
|
755
852
|
return true
|
756
853
|
end
|
757
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
854
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isRefutedBy') then
|
758
855
|
return true
|
759
856
|
end
|
760
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
857
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isSourceOf') then
|
761
858
|
return true
|
762
859
|
end
|
763
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
860
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isSpatiotemporallyRelatedTo') then
|
764
861
|
return true
|
765
862
|
end
|
766
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
863
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isSupportedBy') then
|
767
864
|
return true
|
768
865
|
end
|
769
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
866
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#isTemporarilyPartOf') then
|
770
867
|
return true
|
771
868
|
end
|
772
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
869
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#references') then
|
773
870
|
return true
|
774
871
|
end
|
775
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
872
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#refersTo') then
|
776
873
|
return true
|
777
874
|
end
|
778
875
|
return false
|
@@ -782,212 +879,233 @@ class GFVO
|
|
782
879
|
#
|
783
880
|
# +uri+:: URI that is tested for being a datatype property
|
784
881
|
def self.is_datatype_property?(uri)
|
785
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
882
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#hasValue') then
|
786
883
|
return true
|
787
884
|
end
|
788
|
-
|
885
|
+
return false
|
886
|
+
end
|
887
|
+
|
888
|
+
# Determines whether the given URI is a class.
|
889
|
+
#
|
890
|
+
# +uri+:: URI that is tested for being a class
|
891
|
+
def self.is_class?(uri)
|
892
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Alias') then
|
789
893
|
return true
|
790
894
|
end
|
791
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
895
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#AlleleFrequency') then
|
792
896
|
return true
|
793
897
|
end
|
794
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
898
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#AminoAcid') then
|
795
899
|
return true
|
796
900
|
end
|
797
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
901
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#AncestralSequence') then
|
798
902
|
return true
|
799
903
|
end
|
800
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
904
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ArrayComparativeGenomicHybridization') then
|
801
905
|
return true
|
802
906
|
end
|
803
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
907
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Attribute') then
|
804
908
|
return true
|
805
909
|
end
|
806
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
910
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#AverageCoverage') then
|
807
911
|
return true
|
808
912
|
end
|
809
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
913
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#BiologicalEntity') then
|
810
914
|
return true
|
811
915
|
end
|
812
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
916
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#BiopolymerSequencing') then
|
813
917
|
return true
|
814
918
|
end
|
815
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
919
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Breakpoint') then
|
816
920
|
return true
|
817
921
|
end
|
818
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
922
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Catalog') then
|
819
923
|
return true
|
820
924
|
end
|
821
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
925
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Cell') then
|
822
926
|
return true
|
823
927
|
end
|
824
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
928
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ChemicalEntity') then
|
825
929
|
return true
|
826
930
|
end
|
827
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
931
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Chromosome') then
|
828
932
|
return true
|
829
933
|
end
|
830
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
934
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#CircularHelix') then
|
831
935
|
return true
|
832
936
|
end
|
833
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
937
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#CodingFrameOffset') then
|
834
938
|
return true
|
835
939
|
end
|
836
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
940
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#CodonSequence') then
|
837
941
|
return true
|
838
942
|
end
|
839
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
943
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Collection') then
|
840
944
|
return true
|
841
945
|
end
|
842
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
946
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Comment') then
|
843
947
|
return true
|
844
948
|
end
|
845
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
949
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Contig') then
|
846
950
|
return true
|
847
951
|
end
|
848
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
952
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Coverage') then
|
849
953
|
return true
|
850
954
|
end
|
851
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
955
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#DNAMicroarray') then
|
852
956
|
return true
|
853
957
|
end
|
854
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
958
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#DNASequence') then
|
855
959
|
return true
|
856
960
|
end
|
857
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
961
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#DNASequencing') then
|
858
962
|
return true
|
859
963
|
end
|
860
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
964
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ExperimentalMethod') then
|
861
965
|
return true
|
862
966
|
end
|
863
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
967
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ExternalReference') then
|
864
968
|
return true
|
865
969
|
end
|
866
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
970
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Feature') then
|
867
971
|
return true
|
868
972
|
end
|
869
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
973
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Female') then
|
870
974
|
return true
|
871
975
|
end
|
872
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
976
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#File') then
|
873
977
|
return true
|
874
978
|
end
|
875
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
979
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ForwardReferenceSequenceFrameshift') then
|
876
980
|
return true
|
877
981
|
end
|
878
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
982
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#FragmentReadPlatform') then
|
879
983
|
return true
|
880
984
|
end
|
881
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
985
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#FunctionalSpecification') then
|
882
986
|
return true
|
883
987
|
end
|
884
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
988
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#GameticPhase') then
|
885
989
|
return true
|
886
990
|
end
|
887
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
991
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Genome') then
|
888
992
|
return true
|
889
993
|
end
|
890
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
994
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#GenomeAnalysis') then
|
891
995
|
return true
|
892
996
|
end
|
893
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
997
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#GenomicAscertainingMethod') then
|
894
998
|
return true
|
895
999
|
end
|
896
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1000
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Genotype') then
|
897
1001
|
return true
|
898
1002
|
end
|
899
|
-
|
900
|
-
end
|
901
|
-
|
902
|
-
# Determines whether the given URI is a class.
|
903
|
-
#
|
904
|
-
# +uri+:: URI that is tested for being a class
|
905
|
-
def self.is_class?(uri)
|
906
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#AlignmentOperation') then
|
1003
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Genotyping') then
|
907
1004
|
return true
|
908
1005
|
end
|
909
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1006
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#GermlineCell') then
|
910
1007
|
return true
|
911
1008
|
end
|
912
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1009
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#HelixStructure') then
|
913
1010
|
return true
|
914
1011
|
end
|
915
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1012
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Hemizygous') then
|
916
1013
|
return true
|
917
1014
|
end
|
918
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1015
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Heritage') then
|
919
1016
|
return true
|
920
1017
|
end
|
921
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1018
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Hermaphrodite') then
|
922
1019
|
return true
|
923
1020
|
end
|
924
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1021
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Heterozygous') then
|
925
1022
|
return true
|
926
1023
|
end
|
927
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1024
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Homozygous') then
|
928
1025
|
return true
|
929
1026
|
end
|
930
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1027
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Identifier') then
|
931
1028
|
return true
|
932
1029
|
end
|
933
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1030
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#InformationContentEntity') then
|
934
1031
|
return true
|
935
1032
|
end
|
936
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1033
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Interaction') then
|
937
1034
|
return true
|
938
1035
|
end
|
939
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1036
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Label') then
|
940
1037
|
return true
|
941
1038
|
end
|
942
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1039
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Landmark') then
|
943
1040
|
return true
|
944
1041
|
end
|
945
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1042
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Likelihood') then
|
946
1043
|
return true
|
947
1044
|
end
|
948
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1045
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Locus') then
|
949
1046
|
return true
|
950
1047
|
end
|
951
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1048
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Male') then
|
952
1049
|
return true
|
953
1050
|
end
|
954
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1051
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Match') then
|
955
1052
|
return true
|
956
1053
|
end
|
957
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1054
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#MaterialEntity') then
|
958
1055
|
return true
|
959
1056
|
end
|
960
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1057
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#MaternalHeritage') then
|
961
1058
|
return true
|
962
1059
|
end
|
963
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1060
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#MobileElementSequenceVariant') then
|
964
1061
|
return true
|
965
1062
|
end
|
966
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1063
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Name') then
|
967
1064
|
return true
|
968
1065
|
end
|
969
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1066
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Note') then
|
970
1067
|
return true
|
971
1068
|
end
|
972
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1069
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#NumberOfReads') then
|
1070
|
+
return true
|
1071
|
+
end
|
1072
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Object') then
|
973
1073
|
return true
|
974
1074
|
end
|
975
1075
|
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#PairedEndReadPlatform') then
|
976
1076
|
return true
|
977
1077
|
end
|
978
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1078
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#PaternalHeritage') then
|
1079
|
+
return true
|
1080
|
+
end
|
1081
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#PeptideSequence') then
|
1082
|
+
return true
|
1083
|
+
end
|
1084
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Phenotype') then
|
979
1085
|
return true
|
980
1086
|
end
|
981
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1087
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#PhredScore') then
|
982
1088
|
return true
|
983
1089
|
end
|
984
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1090
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#PrenatalCell') then
|
985
1091
|
return true
|
986
1092
|
end
|
987
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1093
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Process') then
|
988
1094
|
return true
|
989
1095
|
end
|
990
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1096
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ProteinSequence') then
|
1097
|
+
return true
|
1098
|
+
end
|
1099
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Quality') then
|
1100
|
+
return true
|
1101
|
+
end
|
1102
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Quantity') then
|
1103
|
+
return true
|
1104
|
+
end
|
1105
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#RNASequencing') then
|
1106
|
+
return true
|
1107
|
+
end
|
1108
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ReferenceSequence') then
|
991
1109
|
return true
|
992
1110
|
end
|
993
1111
|
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ReferenceSequenceGap') then
|
@@ -996,40 +1114,58 @@ class GFVO
|
|
996
1114
|
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#ReverseReferenceSequenceFrameshift') then
|
997
1115
|
return true
|
998
1116
|
end
|
999
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1117
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Sample') then
|
1000
1118
|
return true
|
1001
1119
|
end
|
1002
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1120
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Scaffold') then
|
1003
1121
|
return true
|
1004
1122
|
end
|
1005
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1123
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Score') then
|
1006
1124
|
return true
|
1007
1125
|
end
|
1008
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1126
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Sequence') then
|
1127
|
+
return true
|
1128
|
+
end
|
1129
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#SequenceAlignment') then
|
1009
1130
|
return true
|
1010
1131
|
end
|
1011
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1132
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#SequenceAlignmentOperation') then
|
1012
1133
|
return true
|
1013
1134
|
end
|
1014
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1135
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#SequenceVariant') then
|
1015
1136
|
return true
|
1016
1137
|
end
|
1017
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1138
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#SequencedIndividual') then
|
1139
|
+
return true
|
1140
|
+
end
|
1141
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#SequencingTechnologyPlatform') then
|
1018
1142
|
return true
|
1019
1143
|
end
|
1020
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1144
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Sex') then
|
1021
1145
|
return true
|
1022
1146
|
end
|
1023
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1147
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#SomaticCell') then
|
1148
|
+
return true
|
1149
|
+
end
|
1150
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Span') then
|
1024
1151
|
return true
|
1025
1152
|
end
|
1026
1153
|
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#TargetSequenceGap') then
|
1027
1154
|
return true
|
1028
1155
|
end
|
1029
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1156
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#TotalNumberOfReads') then
|
1157
|
+
return true
|
1158
|
+
end
|
1159
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#VariantCalling') then
|
1160
|
+
return true
|
1161
|
+
end
|
1162
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Version') then
|
1163
|
+
return true
|
1164
|
+
end
|
1165
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#WatsonCrickHelix') then
|
1030
1166
|
return true
|
1031
1167
|
end
|
1032
|
-
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#
|
1168
|
+
if uri == RDF::URI.new('http://www.biointerchange.org/gfvo#Zygosity') then
|
1033
1169
|
return true
|
1034
1170
|
end
|
1035
1171
|
return false
|
@@ -1065,7 +1201,7 @@ class GFVO
|
|
1065
1201
|
end
|
1066
1202
|
|
1067
1203
|
private
|
1068
|
-
@@parent_properties = { RDF::URI.new('http://www.biointerchange.org/gfvo#alignment') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#annotationObjectProperty') => RDF::URI.new('http://www.w3.org/2002/07/owl#topObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#attribute') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#attributeMethod') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#chromosome') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#contains') => RDF::URI.new('http://www.biointerchange.org/gfvo#setObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#dataSource') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#dbxref') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#derivesFrom') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#effect') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#featureObjectProperty') => RDF::URI.new('http://www.w3.org/2002/07/owl#topObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#featureOntology') => RDF::URI.new('http://www.biointerchange.org/gfvo#setObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#featureType') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#genomicSource') => RDF::URI.new('http://www.biointerchange.org/gfvo#setObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#genotype') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#individual') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#locus') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#ontologyTerm') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#parent') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#phenotypeDescription') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#scoreMethod') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#seqid') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#sequenceAnnotation') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#sequenceVariant') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#sourceMethod') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#species') => RDF::URI.new('http://www.biointerchange.org/gfvo#setObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#structuredAttributes') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#target') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#targetAttributeMethod') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#technologyPlatform') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#type') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureObjectProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#3primeContext') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#5primeContext') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#alias') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#aminoAcid') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') => RDF::URI.new('http://www.w3.org/2002/07/owl#topDataProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#averageCoverage') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#build') => RDF::URI.new('http://www.biointerchange.org/gfvo#setDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#codon') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#comment') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#feature') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#featureDatatypeProperty') => RDF::URI.new('http://www.w3.org/2002/07/owl#topDataProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#fileDatatypeProperty') => RDF::URI.new('http://www.biointerchange.org/gfvo#setDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#fileDate') => RDF::URI.new('http://www.biointerchange.org/gfvo#fileDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#fileVersion') => RDF::URI.new('http://www.biointerchange.org/gfvo#fileDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#frequency') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#gffVersion') => RDF::URI.new('http://www.biointerchange.org/gfvo#fileDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#gtfVersion') => RDF::URI.new('http://www.biointerchange.org/gfvo#fileDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#gvfVersion') => RDF::URI.new('http://www.biointerchange.org/gfvo#fileDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#id') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#isCircular') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#isPhased') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#name') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#note') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#phase') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#phredScore') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#platformClass') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#platformName') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#readIPairSpan') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#readLength') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#reads') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#score') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#sequence') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#setDatatypeProperty') => RDF::URI.new('http://www.w3.org/2002/07/owl#topDataProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#source') => RDF::URI.new('http://www.biointerchange.org/gfvo#featureDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#span') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#tag') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#totalReads') => RDF::URI.new('http://www.biointerchange.org/gfvo#annotationDatatypeProperty') , RDF::URI.new('http://www.biointerchange.org/gfvo#vcfVersion') => 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RDF::URI.new('http://www.biointerchange.org/gfvo#StructuredAttribute') => RDF::URI.new('http://www.biointerchange.org/gfvo#Attribute') , RDF::URI.new('http://www.biointerchange.org/gfvo#TargetSequenceGap') => RDF::URI.new('http://www.biointerchange.org/gfvo#AlignmentOperation') , RDF::URI.new('http://www.biointerchange.org/gfvo#TechnologyPlatform') => RDF::URI.new('http://www.biointerchange.org/gfvo#Annotation') }
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+
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RDF::URI.new('http://www.biointerchange.org/gfvo#Cell') , RDF::URI.new('http://www.biointerchange.org/gfvo#TargetSequenceGap') => RDF::URI.new('http://www.biointerchange.org/gfvo#SequenceAlignmentOperation') , RDF::URI.new('http://www.biointerchange.org/gfvo#TotalNumberOfReads') => RDF::URI.new('http://www.biointerchange.org/gfvo#NumberOfReads') , RDF::URI.new('http://www.biointerchange.org/gfvo#VariantCalling') => RDF::URI.new('http://www.biointerchange.org/gfvo#GenomeAnalysis') , RDF::URI.new('http://www.biointerchange.org/gfvo#Version') => RDF::URI.new('http://www.biointerchange.org/gfvo#Identifier') , RDF::URI.new('http://www.biointerchange.org/gfvo#WatsonCrickHelix') => RDF::URI.new('http://www.biointerchange.org/gfvo#HelixStructure') , RDF::URI.new('http://www.biointerchange.org/gfvo#Zygosity') => RDF::URI.new('http://www.biointerchange.org/gfvo#Quality') }
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1205
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1070
1206
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end
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1071
1207
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