biointerchange 1.0.0 → 1.0.1

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Files changed (27) hide show
  1. checksums.yaml +7 -0
  2. data/.travis.yml +2 -2
  3. data/README.md +7 -6
  4. data/VERSION +1 -1
  5. data/examples/ReaderModelWriterSequenceDiagram.graffle +3073 -0
  6. data/examples/ReaderModelWriterSequenceDiagram.png +0 -0
  7. data/lib/biointerchange/core.rb +63 -58
  8. data/lib/biointerchange/faldo.rb +125 -35
  9. data/lib/biointerchange/genomics/gff3_feature_sequence.rb +36 -0
  10. data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +254 -147
  11. data/lib/biointerchange/genomics/gff3_reader.rb +22 -3
  12. data/lib/biointerchange/genomics/locations.rb +30 -0
  13. data/lib/biointerchange/gfvo.rb +1072 -0
  14. data/lib/biointerchange/phylogenetics/cdao_rdf_ntriples.rb +6 -5
  15. data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb +7 -4
  16. data/lib/biointerchange/writer.rb +138 -2
  17. data/spec/gff3_rdfwriter_spec.rb +5 -6
  18. data/spec/gvf_rdfwriter_spec.rb +5 -6
  19. data/spec/phylogenetics_spec.rb +1 -1
  20. data/web/images/BioInterchange120.png +0 -0
  21. data/web/images/BioInterchange120inv.png +0 -0
  22. data/web/images/BioInterchange160.png +0 -0
  23. data/web/images/BioInterchange160inv.png +0 -0
  24. data/web/images/BioInterchange300inv.png +0 -0
  25. data/web/index.html +5 -1
  26. data/web/ontologies.html +1538 -21
  27. metadata +31 -46
data/lib/biointerchange/phylogenetics/cdao_rdf_ntriples.rb CHANGED
@@ -25,18 +25,19 @@ class CDAORDFWriter < BioInterchange::Writer
25
25
  # Serialize a model as RDF.
26
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  #
27
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  # +model+:: a generic representation of input data that is an instance of BioInterchange::Phylogenetics::TreeSet
28
- def serialize(model)
28
+ # +uri_prefix+:: optional URI prefix that should be used in the RDFization of individuals/class instances
29
+ def serialize(model, uri_prefix = nil)
29
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  model.contents.each { |tree|
30
- serialize_model(model, tree)
31
+ serialize_model(model, tree, uri_prefix)
31
32
  }
32
33
  end
33
34
 
34
35
  protected
35
36
 
36
- def serialize_model(model, tree)
37
+ def serialize_model(model, tree, uri_prefix = nil)
37
38
  graph = RDF::Graph.new
38
- graph.fast_ostream(@ostream) if BioInterchange::skip_rdf_graph
39
- tree_uri = RDF::URI.new(model.uri)
39
+ tree_uri = RDF::URI.new(uri_prefix) if uri_prefix
40
+ tree_uri = RDF::URI.new(model.uri) unless tree_uri
40
41
  if model.date then
41
42
  graph.insert(RDF::Statement.new(tree_uri, RDF::DC.date, RDF::Literal.new(model.date)))
42
43
  end
data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb CHANGED
@@ -26,9 +26,10 @@ class RDFWriter < BioInterchange::Writer
26
26
  # Serializes a model as RDF.
27
27
  #
28
28
  # +model+:: a generic representation of input data that is derived from BioInterchange::TextMining::Document
29
- def serialize(model)
29
+ # +uri_prefix+:: optional URI prefix that should be used in the RDFization of individuals/class instances
30
+ def serialize(model, uri_prefix = nil)
30
31
  if model.instance_of?(BioInterchange::TextMining::Document) then
31
- serialize_document(model)
32
+ serialize_document(model, uri_prefix)
32
33
  else
33
34
  raise BioInterchange::Exceptions::ImplementationWriterError, 'The provided model cannot be serialized at the moment. ' +
34
35
  'Supported classes are BioInterchange::TextMining::Document (and that\'s it for now).'
@@ -97,9 +98,11 @@ private
97
98
  # (http://code.google.com/p/semanticscience/wiki/SIO).
98
99
  #
99
100
  # +model+:: an instance of +BioInterchange::TextMining::Document+
100
- def serialize_document(model)
101
+ # +uri_prefix+:: optional URI prefix that should be used in the RDFization of individuals/class instances
102
+ def serialize_document(model, uri_prefix)
101
103
  graph = RDF::Graph.new
102
- document_uri = RDF::URI.new(model.uri)
104
+ document_uri = RDF::URI.new(uri_prefix) if uri_prefix
105
+ document_uri = RDF::URI.new(model.uri) unless document_uri
103
106
  graph.insert(RDF::Statement.new(document_uri, RDF.type, BioInterchange::SIO.document))
104
107
  model.contents.each { |content|
105
108
  if content.kind_of?(BioInterchange::TextMining::Content)
data/lib/biointerchange/writer.rb CHANGED
@@ -4,6 +4,10 @@ class Writer
4
4
 
5
5
  # Creates a new instance of a writer that will use the provided output stream to serialize object model instances.
6
6
  #
7
+ # When you override this method, please make sure that the parameter `ostream` is assigned to the instance
8
+ # variable `@ostream`. The instance variable `@ostream` will be used by the serialization helper-method
9
+ # `create_triple`.
10
+ #
7
11
  # +ostream+:: instance of IO or derivative class
8
12
  def initialize(ostream)
9
13
  raise BioInterchange::Exceptions::ImplementationWriterError, 'The output stream is not an instance of IO or its subclasses.' unless ostream.kind_of?(IO)
@@ -13,8 +17,140 @@ class Writer
13
17
  # Serializes an object model instance.
14
18
  #
15
19
  # +model+:: an object model instance
16
- def serialize(model)
17
- raise BioInterchange::Exceptions::ImplementationWriterError, 'You must implement this method, which takes an object model and serializes it into the previously provided output stream.'
20
+ # +uri_prefix+:: optional URI prefix that should be used in the RDFization of individuals/class instances
21
+ def serialize(model, uri_prefix = nil)
22
+ raise BioInterchange::Exceptions::ImplementationWriterError, 'You must implement this method, which takes an object model and serializes it into the output stream provided as constructor (\'initialize\') argument.'
23
+ end
24
+
25
+ # Creates a new triple and serializes it.
26
+ #
27
+ # +subject+:: a string or RDF::URI instance denoting the subject of the triple
28
+ # +predicate+:: a string or RDF::URI instance denoting the predicate of the triple
29
+ # +object+:: RDF::URI instance for URIs or other Ruby class for literals
30
+ # +datatype+:: optional datatype describing literal types
31
+ def create_triple(subject, predicate, object, datatype = nil)
32
+ subject_uri = subject
33
+ subject_uri = subject_uri.to_s unless subject_uri.instance_of?(String)
34
+ subject_uri = "<#{subject_uri}>".sub(/\s/, '%20')
35
+
36
+ predicate_uri = predicate
37
+ predicate_uri = predicate_uri.to_s unless predicate_uri.instance_of?(String)
38
+ predicate_uri = "<#{predicate_uri}>".sub(/\s/, '%20')
39
+
40
+ object_representation = nil
41
+ if object.kind_of?(RDF::URI) then
42
+ object_uri = object.to_s
43
+ object_representation = "<#{object_uri}>".sub(/\s/, '%20')
44
+ else
45
+ if datatype then
46
+ # TODO Append type.
47
+ object_representation = "\"#{object.to_s}\"^^<#{datatype.to_s}>"
48
+ else
49
+ object_representation = "\"#{object.to_s}\""
50
+ end
51
+ end
52
+
53
+ begin
54
+ if BioInterchange::format == :turtle then
55
+ serialize_turtle(subject_uri, predicate_uri, object_representation)
56
+ else
57
+ @ostream.puts("#{subject_uri} #{predicate_uri} #{object_representation}")
58
+ end
59
+ rescue Errno::EPIPE
60
+ # Whenever an output pipe disappears, then the user may be happy with what he/she
61
+ # has seen and hit Ctrl-C, or, piped the output through a UNIX command line tool
62
+ # such as "head".
63
+ exit 0
64
+ end
65
+ end
66
+
67
+ # Finishes serializing triples.
68
+ def close
69
+ if BioInterchange::format == :turtle then
70
+ serialize_turtle()
71
+ end
72
+ end
73
+
74
+ # Sets the base URI prefix that is output/used when serializing triples in Turtle.
75
+ def set_base(uri_prefix)
76
+ uri_prefix(nil)
77
+ @prefixes["<#{uri_prefix}"] = '<'
78
+ end
79
+
80
+ # Adds a URI prefix that should be abbreviated when serializing triples in Turtle.
81
+ def add_prefix(uri_prefix, abbreviation_prefix)
82
+ uri_prefix(nil)
83
+ @prefixes["<#{uri_prefix}"] = "#{abbreviation_prefix}:"
84
+ end
85
+
86
+ private
87
+
88
+ # Abbreviates a given URI or returns `nil` when the URI cannot be shortened.
89
+ #
90
+ # +uri+:: URI that should be shortened
91
+ def uri_prefix(uri)
92
+ @prefixes = {
93
+ '<http://biohackathon.org/resource/faldo#' => 'faldo:',
94
+ '<http://purl.obolibrary.org/obo/' => 'obo:',
95
+ '<http://purl.org/dc/terms/' => 'dc:',
96
+ '<http://www.biointerchange.org/gfvo#' => 'gfvo:',
97
+ '<http://www.w3.org/1999/02/22-rdf-syntax-ns#' => 'rdf:',
98
+ '<http://www.w3.org/2000/01/rdf-schema#' => 'rdfs:',
99
+ '<http://www.w3.org/2001/XMLSchema#' => 'xsd:',
100
+ '<http://www.w3.org/2002/07/owl#' => 'owl:'
101
+ } unless @prefixes
102
+
103
+ return nil unless uri
104
+
105
+ @prefixes.keys.each { |prefix|
106
+ return prefix if uri.start_with?(prefix)
107
+ }
108
+ nil
109
+ end
110
+
111
+ # Returns a Turtle line for the previous triple that is serialized (not the current triple).
112
+ def serialize_turtle(subject_uri = nil, predicate_uri = nil, object_representation = nil)
113
+ unless @last_triple then
114
+ @last_triple = [ subject_uri, predicate_uri, object_representation ]
115
+ @last_triple_identical = [ false, false ]
116
+ @prefixes.each_pair { |prefix_uri, prefix_abbreviation|
117
+ @ostream.puts("@prefix #{prefix_abbreviation} #{prefix_uri}> .") unless prefix_abbreviation == '<'
118
+ }
119
+ @prefixes.each_pair { |prefix_uri, prefix_abbreviation|
120
+ @ostream.puts("@base #{prefix_uri}> .") if prefix_abbreviation == '<'
121
+ }
122
+ return
123
+ end
124
+ last_uri = [ nil, nil, @last_triple[2] ]
125
+ (0..1).each { |column|
126
+ if @last_triple_identical[column] then
127
+ last_uri[column] = ' '
128
+ else
129
+ last_uri[column] = @last_triple[column]
130
+ end
131
+ }
132
+ @last_triple_identical[0] = @last_triple[0] == subject_uri
133
+ @last_triple_identical[1] = @last_triple_identical[0] == true && @last_triple[1] == predicate_uri
134
+ mark = '.'
135
+ mark = ';' if @last_triple_identical[0] == true and @last_triple_identical[1] == false
136
+ mark = ',' if @last_triple_identical[0] == true and @last_triple_identical[1] == true
137
+ (0..2).each { |column|
138
+ uri_prefix = uri_prefix(last_uri[column])
139
+ if uri_prefix then
140
+ abbrev = @prefixes[uri_prefix]
141
+ if abbrev == '<'
142
+ last_uri[column] = last_uri[column].sub(uri_prefix, @prefixes[uri_prefix])
143
+ else
144
+ last_uri[column] = last_uri[column].sub(uri_prefix, @prefixes[uri_prefix])[0..-2]
145
+ end
146
+ end
147
+ }
148
+ # In Turtle, 'rdf:type' can also be written as 'a':
149
+ last_uri[1] = 'a' if last_uri[1] == 'rdf:type'
150
+ @ostream.puts("#{last_uri[0]} #{last_uri[1]} #{last_uri[2]} #{mark}")
151
+ @last_triple[0] = subject_uri
152
+ @last_triple[1] = predicate_uri
153
+ @last_triple[2] = object_representation
18
154
  end
19
155
 
20
156
  end
data/spec/gff3_rdfwriter_spec.rb CHANGED
@@ -7,7 +7,7 @@ require 'rspec'
7
7
  # is true, but they are only "re-initialized" with the very same values.
8
8
  v, $VERBOSE = $VERBOSE, nil
9
9
  load 'lib/biointerchange/core.rb'
10
- load 'lib/biointerchange/gff3o.rb'
10
+ load 'lib/biointerchange/gfvo.rb'
11
11
  load 'lib/biointerchange/sofa.rb'
12
12
  load 'lib/biointerchange/reader.rb'
13
13
  load 'lib/biointerchange/model.rb'
@@ -15,6 +15,7 @@ load 'lib/biointerchange/writer.rb'
15
15
  load 'lib/biointerchange/genomics/gff3_rdf_ntriples.rb'
16
16
  load 'lib/biointerchange/genomics/gff3_feature_set.rb'
17
17
  load 'lib/biointerchange/genomics/gff3_feature.rb'
18
+ load 'lib/biointerchange/genomics/gff3_feature_sequence.rb'
18
19
  $VERBOSE = v
19
20
 
20
21
  describe BioInterchange::Genomics::RDFWriter do
@@ -23,7 +24,7 @@ describe BioInterchange::Genomics::RDFWriter do
23
24
  istream, ostream = IO.pipe
24
25
  BioInterchange::Genomics::RDFWriter.new(ostream).serialize(BioInterchange::Genomics::GFF3FeatureSet.new())
25
26
  ostream.close
26
- istream.read.lines.count.should eq(1)
27
+ istream.read.lines.count.should eq(10)
27
28
  end
28
29
 
29
30
  it 'model with three features' do
@@ -70,11 +71,9 @@ describe BioInterchange::Genomics::RDFWriter do
70
71
  lines = istream.read.lines
71
72
  feature_no = 0
72
73
  lines.each { |line|
73
- subject, predicate, object = line.chomp.split(/\s/, 3)
74
- object.sub!(/\s+\.$/, '')
75
- feature_no += 1 if predicate == "<#{RDF.type}>" and object == "<#{BioInterchange::GFF3O.Feature}>"
74
+ feature_no += 1 if line.match(/\sa\s+gfvo:Feature\s+[.,;]$/)
76
75
  }
77
- lines.count.should be == 37
76
+ lines.count.should be == 64
78
77
  feature_no.should be == 3
79
78
  end
80
79
  end
data/spec/gvf_rdfwriter_spec.rb CHANGED
@@ -7,7 +7,7 @@ require 'rspec'
7
7
  # is true, but they are only "re-initialized" with the very same values.
8
8
  v, $VERBOSE = $VERBOSE, nil
9
9
  load 'lib/biointerchange/core.rb'
10
- load 'lib/biointerchange/gvf1o.rb'
10
+ load 'lib/biointerchange/gfvo.rb'
11
11
  load 'lib/biointerchange/sofa.rb'
12
12
  load 'lib/biointerchange/reader.rb'
13
13
  load 'lib/biointerchange/model.rb'
@@ -18,6 +18,7 @@ load 'lib/biointerchange/genomics/gvf_feature.rb'
18
18
  load 'lib/biointerchange/genomics/gff3_rdf_ntriples.rb'
19
19
  load 'lib/biointerchange/genomics/gff3_feature_set.rb'
20
20
  load 'lib/biointerchange/genomics/gff3_feature.rb'
21
+ load 'lib/biointerchange/genomics/gff3_feature_sequence.rb'
21
22
  $VERBOSE = v
22
23
 
23
24
  describe BioInterchange::Genomics::RDFWriter do
@@ -26,7 +27,7 @@ describe BioInterchange::Genomics::RDFWriter do
26
27
  istream, ostream = IO.pipe
27
28
  BioInterchange::Genomics::RDFWriter.new(ostream).serialize(BioInterchange::Genomics::GVFFeatureSet.new())
28
29
  ostream.close
29
- istream.read.lines.count.should eq(1)
30
+ istream.read.lines.count.should eq(10)
30
31
  end
31
32
 
32
33
  it 'model with three features' do
@@ -70,11 +71,9 @@ describe BioInterchange::Genomics::RDFWriter do
70
71
  lines = istream.read.lines
71
72
  feature_no = 0
72
73
  lines.each { |line|
73
- subject, predicate, object = line.chomp.split(/\s/, 3)
74
- object.sub!(/\s+\.$/, '')
75
- feature_no += 1 if predicate == "<#{RDF.type}>" and object == "<#{BioInterchange::GVF1O.Feature}>"
74
+ feature_no += 1 if line.match(/\sa\s+gfvo:Feature\s+[.,;]$/)
76
75
  }
77
- lines.count.should be == 37
76
+ lines.count.should be == 64
78
77
  feature_no.should be == 3
79
78
  end
80
79
  end
data/spec/phylogenetics_spec.rb CHANGED
@@ -72,7 +72,7 @@ describe BioInterchange::Phylogenetics::CDAORDFWriter do
72
72
  model = BioInterchange::Phylogenetics::NewickReader.new().deserialize('(A,B,(C,D,E)F)G;')
73
73
  BioInterchange::Phylogenetics::CDAORDFWriter.new(ostream).serialize(model)
74
74
  ostream.close
75
- istream.read.lines.count.should eq(151)
75
+ istream.read.lines.count.should eq(103)
76
76
  end
77
77
  end
78
78
  end
data/web/images/BioInterchange120.png ADDED
Binary file
data/web/images/BioInterchange120inv.png ADDED
Binary file
data/web/images/BioInterchange160.png ADDED
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data/web/images/BioInterchange160inv.png ADDED
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data/web/images/BioInterchange300inv.png ADDED
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data/web/index.html CHANGED
@@ -48,8 +48,12 @@
48
48
  <div class="hero-unit">
49
49
  <div style="float: left; margin-right: 24px;"><a href="http://www.biointerchange.org"><img width=150 height=150 src="images/BioInterchange300.png" /></a></div>
50
50
  <h1>BioInterchange</h1>
51
- <p>Interchange data using the Resource Description Framework (RDF) and let BioInterchange automagically create RDF triples from your TSV, XML, GFF3, GVF, Newick and other files. BioInterchange helps you transform your data sets into linked data for sharing and data integration via command line, web-service, or API.</p>
51
+ <p>Interchange data using the Resource Description Framework (RDF) and let BioInterchange automagically create RDF triples from your TSV, XML, GFF3, GVF, Newick and other files. BioInterchange helps you transform your data sets into linked data for sharing and data integration via command line, web-service, or API.<div class="alert alert-info" style="text-align: center;"><a class="icon-warning-sign"></a><i>&nbsp;We are currently moving over to <a href="ontologies.html" style="font-weight: bold;">GFVO</a> for converting GFF3, GTF, GVF and VCF files to RDF.</i></div></p>
52
52
  <!-- <p><a class="btn btn-primary btn-large">Learn more &raquo;</a></p> -->
53
+ <div style="float: right;">
54
+ <a href="https://twitter.com/BioInterchange" class="twitter-follow-button" data-show-count="false" data-size="large">Follow @BioInterchange</a>
55
+ <script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+'://platform.twitter.com/widgets.js';fjs.parentNode.insertBefore(js,fjs);}}(document, 'script', 'twitter-wjs');</script>
56
+ </div>
53
57
  </div>
54
58
 
55
59
  <div class="row">
data/web/ontologies.html CHANGED
@@ -17,6 +17,12 @@
17
17
  </style>
18
18
  <link href="bootstrap/css/bootstrap-responsive.css" rel="stylesheet">
19
19
 
20
+ <script type="text/javascript">
21
+ // Magic Sauce. See https://github.com/twitter/bootstrap/issues/1768
22
+ var shiftWindow = function() { scrollBy(0, -50) };
23
+ if (location.hash) shiftWindow();
24
+ window.addEventListener("hashchange", shiftWindow);
25
+ </script>
20
26
  <!-- Le HTML5 shim, for IE6-8 support of HTML5 elements -->
21
27
  <!--[if lt IE 9]>
22
28
  <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
@@ -48,28 +54,1539 @@
48
54
  <!-- Example row of columns -->
49
55
  <div class="row">
50
56
  <div class="span12">
51
- <h2>Ontologies</h2>
52
- <p>BioInterchange makes use of external ontologies, i.e. ontologies that were developed outside the scope of the BioInterchange project, as well as ontologies that we designed and implemented for specific file format conversion purposes. We are always happy to hear about ontologies that we should consider incorporating into BioInterchange and contributions of ontologies that permit including more file formats for RDF conversion are most welcome.</p>
57
+ <h2>Overview</h2>
58
+ <p>BioInterchange makes use of several external ontologies, i.e. ontologies that were developed outside the scope of the BioInterchange project. We are always happy to hear about ontologies that we should consider incorporating into BioInterchange and we welcome contributions of ontologies that permit including more file formats for RDF conversion.</p>
59
+ <p>External ontologies used in BioInterchange:
60
+ <ul>
61
+ <li><a href="http://sourceforge.net/apps/mediawiki/cdao/index.php?title=Main_Page">Comparative Data Analysis Ontology</a> (CDAO)</li>
62
+ <li><a href="https://github.com/JervenBolleman/FALDO">Feature Annotation Location Description Ontology</a> (FALDO)</li>
63
+ <li><a href="http://xmlns.com/foaf/spec">Friend of a Friend</a> (FOAF)</li>
64
+ <li><a href="http://code.google.com/p/semanticscience/wiki/SIO">Semanticscience Integrated Ontology</a> (SIO)</li>
65
+ </ul>
66
+ </p>
67
+ <p>One particular ontology &mdash; the Genomic Feature and Variation Ontology &mdash; that we will be using in the next release of BioInterchange for converting <a href="http://www.sequenceontology.org/resources/gff3.html">GFF3</a>, <a href="http://www.sequenceontology.org/resources/gvf.html">GVF</a>, <a href="http://www.ensembl.org/info/website/upload/gff.html">GTF</a>, and <a href="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41">VCF</a> file formats into RDF is described below. The current version of BioInterchange makes use of <a href="https://github.com/BioInterchange/Ontologies">GFF3O</a> and <a href="https://github.com/BioInterchange/Ontologies">GVF1O</a>, which were merged into GFVO.
53
68
  <p>The <b>BioInterchange vocabulary wrappers</b> that are available for Ruby, Python and Java, are described as part of the <a href="api.html">API</a> documentation.</p>
54
- <h3>BioInterchange Ontologies</h3>
55
- Some ontologies have been specifically designed and implemented for BioInterchange and are freely available via the <a href="http://creativecommons.org/licenses/by-sa/3.0/">Creative Commons Attribution Share-Alike</a> (<a href="http://creativecommons.org/licenses/by-sa/3.0/">CC BY-SA</a>) license. The listing below gives an overview of the ontologies we created, where more information about them is available on their <a href="http://biointerchange.github.com/Ontologies">GitHub project pages</a>.
56
- <h4>Generic Feature Format Version 3 Ontology</h4>
57
- <p>The Generic Feature Format Version 3 Ontology (GFF3O) has been closely modelled on the <a href="http://www.sequenceontology.org/resources/gff3.html">Generic Feature Format Version 3</a> (GFF3) specification.</p>
58
- <ul>
59
- <li><a href="http://biointerchange.github.com/Ontologies">Generic Feature Format Version 3 Ontology</a> (GFF3O)</li>
60
- </ul>
61
- <h4>Genome Variation Format Version 1 Ontology</h4>
62
- <p>The Genome Variation Format Version 1 Ontology (GVF1O) has been closely modelled on the <a href="http://www.sequenceontology.org/resources/gvf.html">Genomic Variation Format</a> (GVF) specification.</p>
63
- <ul>
64
- <li><a href="http://biointerchange.github.com/Ontologies">Genome Variation Format Version 1 Ontology</a> (GVF1O)</li>
65
- </ul>
66
- <h3>External Ontologies</h3>
67
- <ul>
68
- <li><a href="http://sourceforge.net/apps/mediawiki/cdao/index.php?title=Main_Page">Comparative Data Analysis Ontology</a> (CDAO)</li>
69
- <li><a href="https://github.com/JervenBolleman/FALDO">Feature Annotation Location Description Ontology</a> (FALDO)</li>
70
- <li><a href="http://xmlns.com/foaf/spec">Friend of a Friend</a> (FOAF)</li>
71
- <li><a href="http://code.google.com/p/semanticscience/wiki/SIO">Semanticscience Integrated Ontology</a> (SIO)</li>
72
- </ul>
69
+ <h2>Genomic Feature and Variation Ontology (GFVO)</h2>
70
+ <p>The Genomic Feature and Variation Ontology (GFVO) enables the RDFization of genomic feature and variation data. It particularly addresses the representation of data in <a href="http://www.sequenceontology.org/resources/gff3.html">GFF3</a>, <a href="http://www.sequenceontology.org/resources/gvf.html">GVF</a>, <a href="http://www.ensembl.org/info/website/upload/gff.html">GTF</a>, and <a href="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41">VCF</a> formats (the latter two representation are still in development).</p>
71
+ <p>GFVO can be loaded into <a href="http://protege.stanford.edu">Prot&eacute;g&eacute;</a> or <a href="http://www.topquadrant.com/products/TB_Composer.html">TopBraid Composer</a> via: <a href="http://www.biointerchange.org/gfvo">http://www.biointerchange.org/gfvo</a></p>
72
+ <ol>
73
+ <li><a href="#external">External Ontologies and Linked Data</a></li>
74
+ <li><a href="#examples">Examples</a></li>
75
+ <ol style="list-style-type: lower-alpha;">
76
+ <li><a href="#example1">Example 1: Loci and Basic Genomic Feature Annotations</a></li>
77
+ <li><a href="#example1">Example 2: Encoding of a Sequence Alignment</a></li>
78
+ </ol>
79
+ </ol>
80
+ <div class="alert alert-info"><p><b>Note: </b> <span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span>and <span style="margin-right: 4px;" class="badge badge-warning">VCF</span> badges indicate a particular class or property definition's origin. The application of the class or property is not restricted to those file formats though.</p></div>
81
+ <p>GFVO is being developed as the joint work of <a href="http://joachimbaran.wordpress.com">Joachim Baran</a> (<i>corresponding author</i>, <i>joachim.baran</i><b>&#64;</b><i>gmail.com</i>), <a href="http://utah.academia.edu/BDurgahee">Begum Durgahee</a>, <a href="http://medicine.utah.edu/faculty/mddetail.php?facultyID=u0514925">Karen Eilbeck</a>, <a href="http://ntnu-no.academia.edu/ErickAntezana">Erick Antezana</a>, <a href="http://leechuck.de">Robert Hoehndorf</a>, and <a href="http://dumontierlab.com">Michel Dumontier</a>.</p>
82
+ <p>Feedback on the ontology has been provided by <a href="http://www.linkedin.com/in/raoulbonnal">Raoul Bonnal</a>, <a href="http://www.linkedin.com/in/francescostrozzi">Francesco Strozzi</a>, and <a href="http://www.linkedin.com/in/toshiakikatayama">Toshiaki Katayama</a>.</p>
83
+ <h3 id="external">External Ontologies and Linked Data</h3>
84
+ <p>GFVO makes use of the <a href="https://github.com/JervenBolleman/FALDO">Feature Annotation Location Description Ontology</a> (<a href="https://github.com/JervenBolleman/FALDO">FALDO</a>) for describing genomic locations such as genomic features, breakpoints, and coordinate ranges for fuzzy/probabilistic coordinate ranges. We also integrate the <a href="http://variationontology.org">Variation Ontology</a> (<a href="http://variationontology.org">VariO</a>) for describing variants, their effects and conseuences.</p>
85
+ <p>Species are represented as linked data by URIs to NCBI's <a href="http://www.ncbi.nlm.nih.gov/taxonomy">species taxonomy</a>. We encourage the use of <a href="http://identifiers.org">identifiers.org</a> URIs for other entities, which will be automatically be supported in the BioInterchange's RDF output with its next release.</p>
86
+ <h3 id="examples">Examples</h3>
87
+ <h4 id="example1">Example 1: Loci and Basic Genomic Feature Annotations</h4>
88
+ <p>Encoding loci and basic genomic feature annotations. The example covers lines 0-3 of the example gene description given in the <a href="http://www.sequenceontology.org/resources/gff3.html">GFF3 specification</a>.</p>
89
+ <pre style="font-size: 10px; line-height: 13px;">
90
+ @prefix : &lt;http://www.biointerchange.org/gfvo#&gt; .
91
+ @prefix dc: &lt;http://purl.org/dc/terms/&gt; .
92
+ @prefix owl: &lt;http://www.w3.org/2002/07/owl#&gt; .
93
+ @prefix rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; .
94
+ @prefix xml: &lt;http://www.w3.org/XML/1998/namespace&gt; .
95
+ @prefix xsd: &lt;http://www.w3.org/2001/XMLSchema#&gt; .
96
+ @prefix rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; .
97
+ @prefix faldo: &lt;http://biohackathon.org/resource/faldo#&gt; .
98
+ @prefix vario: &lt;http://purl.obolibrary.org/obo/&gt; .
99
+ @base &lt;http://www.biointerchange.org/gfvo#&gt; .
100
+
101
+ #################################################################
102
+ #
103
+ # Example 1
104
+ #
105
+ # Encoding loci and basic genomic feature annotations. The
106
+ # example covers lines 0-3 of the example gene description
107
+ # given in the GFF3 specification.
108
+ # (http://www.sequenceontology.org/resources/gff3.html)
109
+ #
110
+ # Please note that this seemingly verbose data representation
111
+ # is slighly misleading. The reuse of non-literals as well as
112
+ # binary RDF encodings such as RDF/HDT permits a more concise
113
+ # representation of the same data.
114
+ #
115
+ #################################################################
116
+
117
+ :ExampleSet1 rdf:type :File ,
118
+ owl:NamedIndividual ;
119
+ :gffVersion "3" ;
120
+ rdfs:comment "A simple example of a hierarchical genomic feature dependency. This example is an excerpt of another example given in the GFF3 specification (http://sequenceontology.org/resources/gff3.html)."@en .
121
+
122
+ :ExampleSet1ChromEnd rdf:type faldo:ExactPosition ,
123
+ owl:NamedIndividual ;
124
+ faldo:position "1497228" .
125
+
126
+ :ExampleSet1ChromStart rdf:type faldo:ExactPosition ,
127
+ owl:NamedIndividual ;
128
+ faldo:position "1" .
129
+
130
+ :ExampleSet1Feature1 rdf:type :Feature ,
131
+ owl:NamedIndividual ;
132
+ :id "gene00001" ;
133
+ :name "EDEN" ;
134
+ :type "http://www.sequenceontology.org/browser/current_release/term/SO:0000704" ;
135
+ :seqid :ExampleSet1Landmark1 .
136
+
137
+ :ExampleSet1Feature1_2Start rdf:type faldo:ExactPosition ,
138
+ owl:NamedIndividual ;
139
+ faldo:position "1000" .
140
+
141
+ :ExampleSet1Feature2 rdf:type :Feature ,
142
+ owl:NamedIndividual ;
143
+ :id "tfbs00001" ;
144
+ :type "http://www.sequenceontology.org/browser/current_release/term/SO:0000235" ;
145
+ :parent :ExampleSet1Feature1 ;
146
+ :locus :ExampleSet1Region3 .
147
+
148
+ :ExampleSet1Feature2End rdf:type faldo:ExactPosition ,
149
+ owl:NamedIndividual ;
150
+ faldo:position "1012" .
151
+
152
+ :ExampleSet1Landmark1 rdf:type :Landmark ,
153
+ owl:NamedIndividual ;
154
+ :id "ctg123" ;
155
+ :locus :ExampleSet1Region1 .
156
+
157
+ :ExampleSet1Region1 rdf:type faldo:Region ,
158
+ owl:NamedIndividual ;
159
+ faldo:begin :ExampleSet1ChromEnd ,
160
+ :ExampleSet1ChromStart .
161
+
162
+ :ExampleSet1Region2 rdf:type faldo:ForwardStrandPosition ,
163
+ owl:NamedIndividual ;
164
+ faldo:begin :ExampleSet1Feature1_2Start ;
165
+ faldo:end :ExampleSet1Feature1End .
166
+
167
+ :ExampleSet1Region3 rdf:type faldo:Region ,
168
+ owl:NamedIndividual ;
169
+ faldo:begin :ExampleSet1Feature1_2Start ;
170
+ faldo:end :ExampleSet1Feature2End .
171
+
172
+ :ExampleSet1Feature1End rdf:type faldo:ExactPosition ,
173
+ owl:NamedIndividual ;
174
+ faldo:position "9000" .
175
+ </pre>
176
+
177
+ <h4 id="example2">Example 2: Encoding of a Sequence Alignment</h4>
178
+ <p>Encoding of a sequence alignment. This is part of the <a href="http://www.sequenceontology.org/resources/gff3.html">GFF3 specification</a>, denoting the alignment between the reference sequence "chr3" and the target sequence "EST23".</p>
179
+ <pre style="font-size: 10px; line-height: 13px;">
180
+ @prefix : &lt;http://www.biointerchange.org/gfvo#&gt; .
181
+ @prefix dc: &lt;http://purl.org/dc/terms/&gt; .
182
+ @prefix owl: &lt;http://www.w3.org/2002/07/owl#&gt; .
183
+ @prefix rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; .
184
+ @prefix xml: &lt;http://www.w3.org/XML/1998/namespace&gt; .
185
+ @prefix xsd: &lt;http://www.w3.org/2001/XMLSchema#&gt; .
186
+ @prefix rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; .
187
+ @prefix faldo: &lt;http://biohackathon.org/resource/faldo#&gt; .
188
+ @prefix vario: &lt;http://purl.obolibrary.org/obo/&gt; .
189
+ @base &lt;http://www.biointerchange.org/gfvo#&gt; .
190
+
191
+ #################################################################
192
+ #
193
+ # Example 2
194
+ #
195
+ # Encoding of a sequence alignment. This is part of the GFF3
196
+ # specification, denoting the alignment between the reference
197
+ # sequence "chr3" and the target sequence "EST23".
198
+ # (http://www.sequenceontology.org/resources/gff3.html)
199
+ #
200
+ #################################################################
201
+
202
+ :ExampleSet2 rdf:type :Set ,
203
+ owl:NamedIndividual ;
204
+ rdfs:comment "An example of a sequence alignment. This example is an excerpt of another example given in the GFF3 specification (http://sequenceontology.org/resources/gff3.html)."@en .
205
+
206
+ :ExampleSet2Feature1 rdf:type :Feature ,
207
+ owl:NamedIndividual ;
208
+ :id "Match1" ;
209
+ :type "http://www.sequenceontology.org/browser/current_release/term/SO:0000343" ;
210
+ :seqid :ExampleSet2Landmark1 .
211
+
212
+ :ExampleSet2Feature2 rdf:type :Feature ,
213
+ owl:NamedIndividual ;
214
+ :id "EST23" ;
215
+ :type "http://www.sequenceontology.org/browser/current_release/term/SO:0000345" ;
216
+ :target :ExampleSet2Target1 .
217
+
218
+ :ExampleSet2Landmark1 rdf:type :Landmark ,
219
+ owl:NamedIndividual ;
220
+ :id "chr3" .
221
+
222
+ :ExampleSet2Target1 rdf:type :Target ,
223
+ owl:NamedIndividual ;
224
+ :alignment :ExampleSet2AlignmentOperation1 .
225
+
226
+ :ExampleSet2AlignmentOperation1 rdf:type :AlignmentOperation ,
227
+ owl:NamedIndividual ;
228
+ :operation :Match ;
229
+ :span "8" ;
230
+ :first :ExampleSet2AlignmentOperation1 ;
231
+ :rest :ExampleSet2AlignmentOperation2 .
232
+
233
+ :ExampleSet2AlignmentOperation2 rdf:type :AlignmentOperation ,
234
+ owl:NamedIndividual ;
235
+ :operation :TargetSequenceGap ;
236
+ :span "3" ;
237
+ :first :ExampleSet2AlignmentOperation2 ;
238
+ :rest :ExampleSet2AlignmentOperation3 .
239
+
240
+ :ExampleSet2AlignmentOperation3 rdf:type :AlignmentOperation ,
241
+ owl:NamedIndividual ;
242
+ :operation :Match ;
243
+ :span "6" ;
244
+ :first :ExampleSet2AlignmentOperation3 ;
245
+ :rest :ExampleSet2AlignmentOperation4 .
246
+
247
+ :ExampleSet2AlignmentOperation4 rdf:type :AlignmentOperation ,
248
+ owl:NamedIndividual ;
249
+ :operation :ReferenceSequenceGap ;
250
+ :span "1" ;
251
+ :first :ExampleSet2AlignmentOperation4 ;
252
+ :rest :ExampleSet2AlignmentOperation5 .
253
+
254
+ :ExampleSet2AlignmentOperation5 rdf:type :AlignmentOperation ,
255
+ owl:NamedIndividual ;
256
+ :operation :Match ;
257
+ :span "6" ;
258
+ :first :ExampleSet2AlignmentOperation5 .
259
+ </pre>
260
+
261
+ <h3 id="ontologyReference">Ontology Reference</h3>
262
+ <!-- Imported via :r!~/src/Ontologies/scripts/xml2htmldocs.rb < ~/src/Ontologies/gfvo.xml -->
263
+
264
+ <p>
265
+ Ontology namespace "gfvo": http://www.biointerchange.org/gfvo#
266
+ </p>
267
+ <h4>Classes</h4>
268
+ <p>
269
+ <h5 id="classAlignmentOperation">Class gfvo:AlignmentOperation</h5>
270
+ <div style="margin-left: 16px; margin-bottom: 16px">
271
+ <div><i>Subclass of:</i> <a href="#classLocusAnnotation">LocusAnnotation</a></div>
272
+ <div><i>Label:</i> Alignment Operation</div>
273
+ <div><i>Comment:</i> An alignment operation captures the type of alignment (see &quot;Alignment&quot; enumeration class) and alignment length between a reference sequence and target sequence. This relationship is typically expressed between a <a href="#classFeature">Feature</a> class instance and a <a href="#classTarget">Target</a> class instance. Note that an <a href="#classAlignmentOperation">Alignment Operation</a> is a list, where the order of the alignment operations is of significance.</div>
274
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
275
+ </div>
276
+ </p>
277
+ <p>
278
+ <h5 id="classArrayComparativeGenomicHybridization">Class gfvo:ArrayComparativeGenomicHybridization</h5>
279
+ <div style="margin-left: 16px; margin-bottom: 16px">
280
+ <div><i>Subclass of:</i> <a href="#classDataSource">DataSource</a></div>
281
+ <div><i>Label:</i> Array Comparative Genomic Hybridization</div>
282
+ <div><i>Comment:</i> A <a href="#classDataSource">Data Source</a> based on array-comparative genomic hybridization.</div>
283
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
284
+ </div>
285
+ </p>
286
+ <p>
287
+ <h5 id="classAttribute">Class gfvo:Attribute</h5>
288
+ <div style="margin-left: 16px; margin-bottom: 16px">
289
+ <div><i>Subclass of:</i> <a href="#classCustomAnnotation">CustomAnnotation</a></div>
290
+ <div><i>Label:</i> Attribute</div>
291
+ <div><i>Comment:</i> An attribute represents a tag/value pair that is not covered by either GFF3, GTF, GVF or VCF specification. For example, lowercase tags in GFF3 are permitted to allow data providers to provide additional information about a genomic feature, variant, or its meta-data. Tag/value pair attributes that are within the aforementioned specifications are expressed using classes such as <a href="#classVariant">Variant</a>, <a href="#classBreakpoint">Breakpoint</a> or <a href="#classTechnologyPlatform">Technology Platform</a>.</div>
292
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
293
+ </div>
294
+ </p>
295
+ <p>
296
+ <h5 id="classBreakpoint">Class gfvo:Breakpoint</h5>
297
+ <div style="margin-left: 16px; margin-bottom: 16px">
298
+ <div><i>Subclass of:</i> <a href="#classLocusAnnotation">LocusAnnotation</a></div>
299
+ <div><i>Label:</i> Breakpoint</div>
300
+ <div><i>Comment:</i> A breakpoint describes the source or destination of a zero-length sequence alteration. These alterations are typically insertions, deletions or translocations according to the GVF specification (see &quot;Breakpoint_detail&quot; in http://sequenceontology.org/resources/gvf.html).</div>
301
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
302
+ </div>
303
+ </p>
304
+ <p>
305
+ <h5 id="classChromosome">Class gfvo:Chromosome</h5>
306
+ <div style="margin-left: 16px; margin-bottom: 16px">
307
+ <div><i>Subclass of:</i> <a href="#classLocusAnnotation">LocusAnnotation</a></div>
308
+ <div><i>Label:</i> Chromosome</div>
309
+ <div><i>Comment:</i> A chromosome is an abstract representation of an unnamed chromosome to represent ploidy within a data set. A <a href="#classChromosome">Chromosome</a> is typically used in conjunction with <a href="#classSequencedIndividual">Sequenced Individual</a> instances. For placing genomic features (<a href="#classFeature">Feature</a> class instances) on a chromosome, contig, scaffold, etc., please see the <a href="#classLandmark">Landmark</a> class.</div>
310
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
311
+ </div>
312
+ </p>
313
+ <p>
314
+ <h5 id="classCustomAnnotation">Class gfvo:CustomAnnotation</h5>
315
+ <div style="margin-left: 16px; margin-bottom: 16px">
316
+ <div><i>Subclass of:</i> <a href="#classFeatureAnnotation">FeatureAnnotation</a></div>
317
+ <div><i>Label:</i> Custom Annotation</div>
318
+ <div><i>Comment:</i> A custom annotation is any additionally provided genomic annotation that is not covered by the GFF3, GTF, GVF or VCF specifications, and hence, not represented by any other class in the ontology. For example, in GFF3, this would typically cover the attributes with lowercase tags of column 9, which are permitted by the standard as user defined annotations.</div>
319
+ <div></div>
320
+ </div>
321
+ </p>
322
+ <p>
323
+ <h5 id="classDNAMicroarray">Class gfvo:DNAMicroarray</h5>
324
+ <div style="margin-left: 16px; margin-bottom: 16px">
325
+ <div><i>Subclass of:</i> <a href="#classDataSource">DataSource</a></div>
326
+ <div><i>Label:</i> DNA Microarray</div>
327
+ <div><i>Comment:</i> A <a href="#classDataSource">Data Source</a> based on DNA microarray probes.</div>
328
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
329
+ </div>
330
+ </p>
331
+ <p>
332
+ <h5 id="classDNASequence">Class gfvo:DNASequence</h5>
333
+ <div style="margin-left: 16px; margin-bottom: 16px">
334
+ <div><i>Subclass of:</i> <a href="#classDataSource">DataSource</a></div>
335
+ <div><i>Label:</i> DNA Sequence</div>
336
+ <div><i>Comment:</i> A <a href="#classDataSource">Data Source</a> based on DNA sequences.</div>
337
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
338
+ </div>
339
+ </p>
340
+ <p>
341
+ <h5 id="classDataSource">Class gfvo:DataSource</h5>
342
+ <div style="margin-left: 16px; margin-bottom: 16px">
343
+ <div><i>Subclass of:</i> <a href="#classTechnologicalAnnotation">TechnologicalAnnotation</a></div>
344
+ <div><i>Label:</i> Data Source</div>
345
+ <div><i>Comment:</i> Provides information about the source of the data. For example, it can link out to actual sequences associated with <a href="#classFeature">Feature</a> individuals in a <a href="#classSet">Set</a>.</div>
346
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
347
+ </div>
348
+ </p>
349
+ <p>
350
+ <h5 id="classEffect">Class gfvo:Effect</h5>
351
+ <div style="margin-left: 16px; margin-bottom: 16px">
352
+ <div><i>Subclass of:</i> <a href="#classVariationAnnotation">VariationAnnotation</a></div>
353
+ <div><i>Label:</i> Effect</div>
354
+ <div><i>Comment:</i> Describing the effect of a feature variant.</div>
355
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
356
+ </div>
357
+ </p>
358
+ <p>
359
+ <h5 id="classFeature">Class gfvo:Feature</h5>
360
+ <div style="margin-left: 16px; margin-bottom: 16px">
361
+ <div><i>Subclass of:</i> <a href="#classRecord">Record</a></div>
362
+ <div><i>Label:</i> Feature</div>
363
+ <div><i>Comment:</i> The feature class captures information about genomic sequence features. A genomic feature can be a large object, such as a chromosome or contig, down to single base-pair reference or variant alleles. A feature class instance is a composite of further information that is encoded using <a href="#classAttribute">Attribute</a>, <a href="#classReference">Reference</a>, &quot;Variation&quot; and other sub-classes of <a href="#classFeatureAnnotation">Feature Annotation</a>.</div>
364
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
365
+ </div>
366
+ </p>
367
+ <p>
368
+ <h5 id="classFeatureAnnotation">Class gfvo:FeatureAnnotation</h5>
369
+ <div style="margin-left: 16px; margin-bottom: 16px">
370
+ <div><i>Subclass of:</i> <a href="#classRecord">Record</a></div>
371
+ <div><i>Label:</i> Feature Annotation</div>
372
+ <div><i>Comment:</i> A feature annotation is a class whose instances are used as composites in conjunction with <a href="#classFeature">Feature</a> class instances. The <a href="#classFeatureAnnotation">Feature Annotation</a> class is typically not used as type annotation. It rather denotes that its subclasses are to be used for extending genomic features with additional information.</div>
373
+ <div></div>
374
+ </div>
375
+ </p>
376
+ <p>
377
+ <h5 id="classFile">Class gfvo:File</h5>
378
+ <div style="margin-left: 16px; margin-bottom: 16px">
379
+ <div><i>Subclass of:</i> <a href="#classSet">Set</a></div>
380
+ <div><i>Label:</i> File</div>
381
+ <div><i>Comment:</i> 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 <a href="#classFile">File</a> class instances should be capture with the generic <a href="#classSet">Set</a> class, which is format independent.</div>
382
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
383
+ </div>
384
+ </p>
385
+ <p>
386
+ <h5 id="classForwardReferenceSequenceFrameshift">Class gfvo:ForwardReferenceSequenceFrameshift</h5>
387
+ <div style="margin-left: 16px; margin-bottom: 16px">
388
+ <div><i>Subclass of:</i> <a href="#classAlignmentOperation">AlignmentOperation</a></div>
389
+ <div><i>Label:</i> Forward Reference Sequence Frameshift</div>
390
+ <div><i>Comment:</i> Denotes a frameshift forward in the reference sequence. The reference sequence is denoted by a <a href="#classLandmark">Landmark</a> whilst the aligned target sequence is an instance of the <a href="#classTarget">Target</a> class.</div>
391
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
392
+ </div>
393
+ </p>
394
+ <p>
395
+ <h5 id="classFragmentReadPlatform">Class gfvo:FragmentReadPlatform</h5>
396
+ <div style="margin-left: 16px; margin-bottom: 16px">
397
+ <div><i>Subclass of:</i> <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
398
+ <div><i>Label:</i> Fragment Read Platform</div>
399
+ <div><i>Comment:</i> Details about the fragment-read sequencing technology used to gather the data in a set.</div>
400
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
401
+ </div>
402
+ </p>
403
+ <p>
404
+ <h5 id="classGermlineFeature">Class gfvo:GermlineFeature</h5>
405
+ <div style="margin-left: 16px; margin-bottom: 16px">
406
+ <div><i>Subclass of:</i> <a href="#classFeature">Feature</a></div>
407
+ <div><i>Label:</i> Germline Feature</div>
408
+ <div><i>Comment:</i> The germline feature class captures information about genomic sequence features arising from germline cells.</div>
409
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
410
+ </div>
411
+ </p>
412
+ <p>
413
+ <h5 id="classHemizygousVariant">Class gfvo:HemizygousVariant</h5>
414
+ <div style="margin-left: 16px; margin-bottom: 16px">
415
+ <div><i>Subclass of:</i> <a href="#classVariant">Variant</a></div>
416
+ <div><i>Label:</i> Hemizygous Variant</div>
417
+ <div><i>Comment:</i> A sequence alteration with hemizygous alleles.</div>
418
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
419
+ </div>
420
+ </p>
421
+ <p>
422
+ <h5 id="classHeterozygousVariant">Class gfvo:HeterozygousVariant</h5>
423
+ <div style="margin-left: 16px; margin-bottom: 16px">
424
+ <div><i>Subclass of:</i> <a href="#classVariant">Variant</a></div>
425
+ <div><i>Label:</i> Heterozygous Variant</div>
426
+ <div><i>Comment:</i> A sequence alteration with heterozygous alleles.</div>
427
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
428
+ </div>
429
+ </p>
430
+ <p>
431
+ <h5 id="classHomozygousVariant">Class gfvo:HomozygousVariant</h5>
432
+ <div style="margin-left: 16px; margin-bottom: 16px">
433
+ <div><i>Subclass of:</i> <a href="#classVariant">Variant</a></div>
434
+ <div><i>Label:</i> Homozygous Variant</div>
435
+ <div><i>Comment:</i> A sequence alteration with homozygous alleles.</div>
436
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
437
+ </div>
438
+ </p>
439
+ <p>
440
+ <h5 id="classLandmark">Class gfvo:Landmark</h5>
441
+ <div style="margin-left: 16px; margin-bottom: 16px">
442
+ <div><i>Subclass of:</i> <a href="#classLocusAnnotation">LocusAnnotation</a></div>
443
+ <div><i>Label:</i> Landmark</div>
444
+ <div><i>Comment:</i> A landmark establishes a coordinate system for features. Landmarks can be chromosomes, contigs, scaffolds or other constructs that can harbor <a href="#classFeature">Feature</a> class instances. For expressing ploidy within a data set, please refer to the <a href="#classChromosome">Chromosome</a> class.</div>
445
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
446
+ </div>
447
+ </p>
448
+ <p>
449
+ <h5 id="classLocusAnnotation">Class gfvo:LocusAnnotation</h5>
450
+ <div style="margin-left: 16px; margin-bottom: 16px">
451
+ <div><i>Subclass of:</i> <a href="#classFeatureAnnotation">FeatureAnnotation</a></div>
452
+ <div><i>Label:</i> Locus Annotation</div>
453
+ <div><i>Comment:</i> A locus annotation puts a genomic feature or variation in context or provides additional information about particular location related aspects that fall within a feature&apos;s range (expressed by the <a href="#objectPropertylocus">locus</a> object property of the <a href="#classFeature">Feature</a> class). The <a href="#classLocusAnnotation">Locus Annotation</a> class is not instantiated itself, but rather one of its subclasses. For example, <a href="#classLandmark">Landmark</a> is used to place a <a href="#classFeature">Feature</a> on a chromosome, scaffold, contig, or other genomic entity.</div>
454
+ <div></div>
455
+ </div>
456
+ </p>
457
+ <p>
458
+ <h5 id="classMatch">Class gfvo:Match</h5>
459
+ <div style="margin-left: 16px; margin-bottom: 16px">
460
+ <div><i>Subclass of:</i> <a href="#classAlignmentOperation">AlignmentOperation</a></div>
461
+ <div><i>Label:</i> Match</div>
462
+ <div><i>Comment:</i> Denotes a match between the reference sequence and target sequence. The reference sequence is denoted by a <a href="#classLandmark">Landmark</a> whilst the aligned target sequence is an instance of the <a href="#classTarget">Target</a> class.</div>
463
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
464
+ </div>
465
+ </p>
466
+ <p>
467
+ <h5 id="classMethod">Class gfvo:Method</h5>
468
+ <div style="margin-left: 16px; margin-bottom: 16px">
469
+ <div><i>Subclass of:</i> <a href="#classTechnologicalAnnotation">TechnologicalAnnotation</a></div>
470
+ <div><i>Label:</i> Method</div>
471
+ <div><i>Comment:</i> Information about the used scoring algorithm or method.</div>
472
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
473
+ </div>
474
+ </p>
475
+ <p>
476
+ <h5 id="classPairedReadPlatform">Class gfvo:PairedReadPlatform</h5>
477
+ <div style="margin-left: 16px; margin-bottom: 16px">
478
+ <div><i>Subclass of:</i> <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
479
+ <div><i>Label:</i> Paired Read Platform</div>
480
+ <div><i>Comment:</i> Details about the paired-read sequencing technology used to gather the data in a set.</div>
481
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
482
+ </div>
483
+ </p>
484
+ <p>
485
+ <h5 id="classPhenotypeDescription">Class gfvo:PhenotypeDescription</h5>
486
+ <div style="margin-left: 16px; margin-bottom: 16px">
487
+ <div><i>Subclass of:</i> <a href="#classSetAnnotation">SetAnnotation</a></div>
488
+ <div><i>Label:</i> Phenotype Description</div>
489
+ <div><i>Comment:</i> A phenotype description represents additional information about a sequenced individual&apos;s phenotype.</div>
490
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
491
+ </div>
492
+ </p>
493
+ <p>
494
+ <h5 id="classPrenatalFeature">Class gfvo:PrenatalFeature</h5>
495
+ <div style="margin-left: 16px; margin-bottom: 16px">
496
+ <div><i>Subclass of:</i> <a href="#classFeature">Feature</a></div>
497
+ <div><i>Label:</i> Prenatal Feature</div>
498
+ <div><i>Comment:</i> A prenatal feature is purportedly associated with prenatal cells; the GVF specification declares this feature type under the prama directive &quot;##genomic-source&quot;, 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 &quot;prenatal&quot; either.</div>
499
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
500
+ </div>
501
+ </p>
502
+ <p>
503
+ <h5 id="classRNASequence">Class gfvo:RNASequence</h5>
504
+ <div style="margin-left: 16px; margin-bottom: 16px">
505
+ <div><i>Subclass of:</i> <a href="#classDataSource">DataSource</a></div>
506
+ <div><i>Label:</i> RNA Sequence</div>
507
+ <div><i>Comment:</i> A <a href="#classDataSource">Data Source</a> based on RNA sequences.</div>
508
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
509
+ </div>
510
+ </p>
511
+ <p>
512
+ <h5 id="classRecord">Class gfvo:Record</h5>
513
+ <div style="margin-left: 16px; margin-bottom: 16px">
514
+ <div><i>Label:</i> Record</div>
515
+ <div><i>Comment:</i> A record is an abstract representation of a genomic feature, genomic variation, or its composite elements. A record is typically not instantiated in itself, but rather its child classes (s.a. <a href="#classFeature">Feature</a>, &quot;Variation&quot;, <a href="#classReference">Reference</a>, etc.) are types for OWL individuals.</div>
516
+ <div></div>
517
+ </div>
518
+ </p>
519
+ <p>
520
+ <h5 id="classReference">Class gfvo:Reference</h5>
521
+ <div style="margin-left: 16px; margin-bottom: 16px">
522
+ <div><i>Subclass of:</i> <a href="#classFeatureAnnotation">FeatureAnnotation</a></div>
523
+ <div><i>Label:</i> Reference</div>
524
+ <div><i>Comment:</i> Denotes the reference sequence of a feature. The reference sequence is of importance when dealing with genomic variation data, which is expressed by the <a href="#classVariant">Variant</a> class.</div>
525
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
526
+ </div>
527
+ </p>
528
+ <p>
529
+ <h5 id="classReferenceSequenceGap">Class gfvo:ReferenceSequenceGap</h5>
530
+ <div style="margin-left: 16px; margin-bottom: 16px">
531
+ <div><i>Subclass of:</i> <a href="#classAlignmentOperation">AlignmentOperation</a></div>
532
+ <div><i>Label:</i> Reference Sequence Gap</div>
533
+ <div><i>Comment:</i> Denotes a gap in the reference sequence for an alignment. The reference sequence is denoted by a <a href="#classLandmark">Landmark</a> whilst the aligned target sequence is an instance of the <a href="#classTarget">Target</a> class.</div>
534
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
535
+ </div>
536
+ </p>
537
+ <p>
538
+ <h5 id="classReverseReferenceSequenceFrameshift">Class gfvo:ReverseReferenceSequenceFrameshift</h5>
539
+ <div style="margin-left: 16px; margin-bottom: 16px">
540
+ <div><i>Subclass of:</i> <a href="#classAlignmentOperation">AlignmentOperation</a></div>
541
+ <div><i>Label:</i> Reverse Reference Sequence Frameshift</div>
542
+ <div><i>Comment:</i> Denotes a frameshift backwards (reverse) in the reference sequence. The reference sequence is denoted by a <a href="#classLandmark">Landmark</a> whilst the aligned target sequence is an instance of the <a href="#classTarget">Target</a> class.</div>
543
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
544
+ </div>
545
+ </p>
546
+ <p>
547
+ <h5 id="classSequencedFemale">Class gfvo:SequencedFemale</h5>
548
+ <div style="margin-left: 16px; margin-bottom: 16px">
549
+ <div><i>Subclass of:</i> <a href="#classSequencedIndividual">SequencedIndividual</a></div>
550
+ <div><i>Label:</i> Sequenced Female</div>
551
+ <div><i>Comment:</i> Aggregated sequencing information for a particular female individual. A female is defined as an individual producing ova.</div>
552
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
553
+ </div>
554
+ </p>
555
+ <p>
556
+ <h5 id="classSequencedHermaphrodite">Class gfvo:SequencedHermaphrodite</h5>
557
+ <div style="margin-left: 16px; margin-bottom: 16px">
558
+ <div><i>Subclass of:</i> <a href="#classSequencedIndividual">SequencedIndividual</a></div>
559
+ <div><i>Label:</i> Sequenced Hermaphrodite</div>
560
+ <div><i>Comment:</i> Aggregated sequencing information for a particular individual that contains both male and female gemetes.</div>
561
+ <div></div>
562
+ </div>
563
+ </p>
564
+ <p>
565
+ <h5 id="classSequencedIndividual">Class gfvo:SequencedIndividual</h5>
566
+ <div style="margin-left: 16px; margin-bottom: 16px">
567
+ <div><i>Subclass of:</i> <a href="#classFeatureAnnotation">FeatureAnnotation</a></div>
568
+ <div><i>Label:</i> Sequenced Individual</div>
569
+ <div><i>Comment:</i> Aggregated sequencing information for a particular individual. Unless a sub-type of this class is used as instance type, s.a. <a href="#classSequencedFemale">Sequenced Female</a>, the sex of the individual is considered to be undetermined.</div>
570
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
571
+ </div>
572
+ </p>
573
+ <p>
574
+ <h5 id="classSequencedMale">Class gfvo:SequencedMale</h5>
575
+ <div style="margin-left: 16px; margin-bottom: 16px">
576
+ <div><i>Subclass of:</i> <a href="#classSequencedIndividual">SequencedIndividual</a></div>
577
+ <div><i>Label:</i> Sequenced Male</div>
578
+ <div><i>Comment:</i> Aggregated sequencing information for a particular male individual. A male is defined as an individual producing spermatozoa.</div>
579
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
580
+ </div>
581
+ </p>
582
+ <p>
583
+ <h5 id="classSet">Class gfvo:Set</h5>
584
+ <div style="margin-left: 16px; margin-bottom: 16px">
585
+ <div><i>Label:</i> Set</div>
586
+ <div><i>Comment:</i> A set is a container for genomic sequence features and related information that is independent of data provenance. A set may contain information about any genomic features including -- but not limited to -- contents of GFF3, GTF, GVF and VCF files. The latter are better represented by <a href="#classFile">File</a> class instances, whereas the result of unions or intersections between different <a href="#classFile">File</a> class instances should be captured within this format-independent <a href="#classSet">Set</a> class.</div>
587
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
588
+ </div>
589
+ </p>
590
+ <p>
591
+ <h5 id="classSetAnnotation">Class gfvo:SetAnnotation</h5>
592
+ <div style="margin-left: 16px; margin-bottom: 16px">
593
+ <div><i>Subclass of:</i> <a href="#classRecord">Record</a></div>
594
+ <div><i>Label:</i> Set Annotation</div>
595
+ <div><i>Comment:</i> A set annotation denotes that its subclasses can be used to extend a <a href="#classSet">Set</a> with additional information, s.a. a <a href="#classPhenotypeDescription">Phenotype Description</a>. Set annotations are file format independent and can be preserved when carrying out operations between <a href="#classFile">File</a>/<a href="#classSet">Set</a> instances. Depending on the annotation, it may or may not be able to carry it over in operations such as taking the union of two or more sets, since the scope of a <a href="#classSetAnnotation">Set Annotation</a> applies to all <a href="#classFeature">Feature</a> instances within the resulting <a href="#classSet">Set</a>.</div>
596
+ <div></div>
597
+ </div>
598
+ </p>
599
+ <p>
600
+ <h5 id="classSomaticFeature">Class gfvo:SomaticFeature</h5>
601
+ <div style="margin-left: 16px; margin-bottom: 16px">
602
+ <div><i>Subclass of:</i> <a href="#classFeature">Feature</a></div>
603
+ <div><i>Label:</i> Somatic Feature</div>
604
+ <div><i>Comment:</i> The somatic feature class captures information about genomic sequence features arising from somatic cells.</div>
605
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
606
+ </div>
607
+ </p>
608
+ <p>
609
+ <h5 id="classStructuredAttribute">Class gfvo:StructuredAttribute</h5>
610
+ <div style="margin-left: 16px; margin-bottom: 16px">
611
+ <div><i>Subclass of:</i> <a href="#classCustomAnnotation">CustomAnnotation</a></div>
612
+ <div><i>Label:</i> Structured Attribute</div>
613
+ <div><i>Comment:</i> 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 &quot;Structured Pragmas&quot; 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 <a href="#classStructuredAttribute">Structured Attribute</a> class is used as well to capture the non-exhaustive list of possible data assignments of the GVF specification.</div>
614
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
615
+ </div>
616
+ </p>
617
+ <p>
618
+ <h5 id="classTarget">Class gfvo:Target</h5>
619
+ <div style="margin-left: 16px; margin-bottom: 16px">
620
+ <div><i>Subclass of:</i> <a href="#classLocusAnnotation">LocusAnnotation</a></div>
621
+ <div><i>Label:</i> Target</div>
622
+ <div><i>Comment:</i> A target expresses the relationship between a <a href="#classFeature">Feature</a> instance and an alignment. In GFF3, the alignment can be a nucleotide-to-nucleotide or protein-to-nucleotide (see &quot;The Gap Attribute&quot;, http://sequenceontology.org/resources/gff3.html), but this restriction is not enforced here. Note that the object property <a href="#objectPropertyalignment">alignment</a> links out to a list of <a href="#classAlignmentOperation">Alignment Operation</a> class instances, where only the first operation in that list is referenced via the <a href="#objectPropertyalignment">alignment</a> property. The remainder of operations can be accessed by stepping through the list.</div>
623
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
624
+ </div>
625
+ </p>
626
+ <p>
627
+ <h5 id="classTargetSequenceGap">Class gfvo:TargetSequenceGap</h5>
628
+ <div style="margin-left: 16px; margin-bottom: 16px">
629
+ <div><i>Subclass of:</i> <a href="#classAlignmentOperation">AlignmentOperation</a></div>
630
+ <div><i>Label:</i> Target Sequence Gap</div>
631
+ <div><i>Comment:</i> Denotes a gap in the target sequence for an alignment. The reference sequence is denoted by a <a href="#classLandmark">Landmark</a> whilst the aligned target sequence is an instance of the <a href="#classTarget">Target</a> class.</div>
632
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
633
+ </div>
634
+ </p>
635
+ <p>
636
+ <h5 id="classTechnologicalAnnotation">Class gfvo:TechnologicalAnnotation</h5>
637
+ <div style="margin-left: 16px; margin-bottom: 16px">
638
+ <div><i>Subclass of:</i> <a href="#classFeatureAnnotation">FeatureAnnotation</a></div>
639
+ <div><i>Label:</i> Technological Annotation</div>
640
+ <div><i>Comment:</i> A technological annotation provides meta-data about the means that led to a genomic feature or variant discovery. This can be a provenance annotation, such as <a href="#classDataSource">Data Source</a>, it can be describing a <a href="#classMethod">Method</a>, or it can be information about the <a href="#classTechnologyPlatform">Technology Platform</a> used.</div>
641
+ <div></div>
642
+ </div>
643
+ </p>
644
+ <p>
645
+ <h5 id="classTechnologyPlatform">Class gfvo:TechnologyPlatform</h5>
646
+ <div style="margin-left: 16px; margin-bottom: 16px">
647
+ <div><i>Subclass of:</i> <a href="#classTechnologicalAnnotation">TechnologicalAnnotation</a></div>
648
+ <div><i>Label:</i> Technology Platform</div>
649
+ <div><i>Comment:</i> Details about the sequencing/microarray technology used to gather the data in a set.</div>
650
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
651
+ </div>
652
+ </p>
653
+ <p>
654
+ <h5 id="classVariant">Class gfvo:Variant</h5>
655
+ <div style="margin-left: 16px; margin-bottom: 16px">
656
+ <div><i>Subclass of:</i> <a href="#classVariationAnnotation">VariationAnnotation</a></div>
657
+ <div><i>Label:</i> Variant</div>
658
+ <div><i>Comment:</i> Describing specific sequence alterations of a genomic feature. A variant is related to <a href="#classReference">Reference</a> class instances, which denote the sequence that serves as a basis for sequence alteration comparisons.</div>
659
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
660
+ </div>
661
+ </p>
662
+ <p>
663
+ <h5 id="classVariationAnnotation">Class gfvo:VariationAnnotation</h5>
664
+ <div style="margin-left: 16px; margin-bottom: 16px">
665
+ <div><i>Subclass of:</i> <a href="#classFeatureAnnotation">FeatureAnnotation</a></div>
666
+ <div><i>Label:</i> Variation Annotation</div>
667
+ <div><i>Comment:</i> A variant annotation captures information about a genomic <a href="#classVariant">Variant</a>. A possible effect of a variant is encoded using <a href="#classEffect">Effect</a> class instances.</div>
668
+ <div></div>
669
+ </div>
670
+ </p>
671
+ <h4>Object Properties (Referencing other Class Instances)</h4>
672
+ <p>
673
+ <h5 id="objectPropertyalignment">Object Property gfvo:alignment</h5>
674
+ <div style="margin-left: 16px; margin-bottom: 16px">
675
+ <div><i>Domain:</i> <a href="#classTarget">Target</a></div>
676
+ <div><i>Range:</i> <a href="#classAlignmentOperation">AlignmentOperation</a></div>
677
+ <div><i>Label:</i> alignment</div>
678
+ <div><i>Comment:</i> An alignment is a sequence alignment between a <a href="#classFeature">Feature</a> class instance and a <a href="#classTarget">Target</a> class instance. The alignment is a list of one or more <a href="#classAlignmentOperation">Alignment Operation</a> instances that capture alignment matches, gaps and frameshifts (see &quot;The Gap Attribute&quot;, http://sequenceontology.org/resources/gff3.html).</div>
679
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
680
+ </div>
681
+ </p>
682
+ <p>
683
+ <h5 id="objectPropertyattributeMethod">Object Property gfvo:attributeMethod</h5>
684
+ <div style="margin-left: 16px; margin-bottom: 16px">
685
+ <div><i>Domain:</i> <a href="#classAttribute">Attribute</a>, <a href="#classBreakpoint">Breakpoint</a>, <a href="#classEffect">Effect</a>, <a href="#classVariant">Variant</a></div>
686
+ <div><i>Range:</i> <a href="#classMethod">Method</a></div>
687
+ <div><i>Label:</i> attribute method</div>
688
+ <div><i>Comment:</i> Further information about the <a href="#classMethod">Method</a> that is related to an attribute.</div>
689
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
690
+ </div>
691
+ </p>
692
+ <p>
693
+ <h5 id="objectPropertyattributes">Object Property gfvo:attributes</h5>
694
+ <div style="margin-left: 16px; margin-bottom: 16px">
695
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
696
+ <div><i>Range:</i> <a href="#classAttribute">Attribute</a></div>
697
+ <div><i>Label:</i> attributes</div>
698
+ <div><i>Comment:</i> Tag name/value pair attributes of a feature.</div>
699
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
700
+ </div>
701
+ </p>
702
+ <p>
703
+ <h5 id="objectPropertybreakpoint">Object Property gfvo:breakpoint</h5>
704
+ <div style="margin-left: 16px; margin-bottom: 16px">
705
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
706
+ <div><i>Range:</i> <a href="#classBreakpoint">Breakpoint</a></div>
707
+ <div><i>Label:</i> breakpoint</div>
708
+ <div><i>Comment:</i> Potential source or destination of zero-length sequence alterations.</div>
709
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
710
+ </div>
711
+ </p>
712
+ <p>
713
+ <h5 id="objectPropertybreakpointObjectProperty">Object Property gfvo:breakpointObjectProperty</h5>
714
+ <div style="margin-left: 16px; margin-bottom: 16px">
715
+ <div><i>Label:</i> breakpoint object property</div>
716
+ <div><i>Comment:</i> A properties that is directly associated with <a href="#classBreakpoint">Breakpoint</a> class instances.</div>
717
+ <div></div>
718
+ </div>
719
+ </p>
720
+ <p>
721
+ <h5 id="objectPropertychromosome">Object Property gfvo:chromosome</h5>
722
+ <div style="margin-left: 16px; margin-bottom: 16px">
723
+ <div><i>Domain:</i> <a href="#classSequencedIndividual">SequencedIndividual</a></div>
724
+ <div><i>Range:</i> <a href="#classChromosome">Chromosome</a></div>
725
+ <div><i>Label:</i> chromosome</div>
726
+ <div><i>Comment:</i> Denotes abstract chromosome representations for capturing variants that appear on the same chromosome of a polyploid organism.</div>
727
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
728
+ </div>
729
+ </p>
730
+ <p>
731
+ <h5 id="objectPropertycontains">Object Property gfvo:contains</h5>
732
+ <div style="margin-left: 16px; margin-bottom: 16px">
733
+ <div><i>Domain:</i> <a href="#classSet">Set</a></div>
734
+ <div><i>Range:</i> <a href="#classFeature">Feature</a></div>
735
+ <div><i>Label:</i> contains</div>
736
+ <div><i>Comment:</i> Relationship that describes which features belong to a feature set.</div>
737
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
738
+ </div>
739
+ </p>
740
+ <p>
741
+ <h5 id="objectPropertydataSource">Object Property gfvo:dataSource</h5>
742
+ <div style="margin-left: 16px; margin-bottom: 16px">
743
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
744
+ <div><i>Range:</i> <a href="#classDataSource">DataSource</a></div>
745
+ <div><i>Label:</i> data source</div>
746
+ <div><i>Comment:</i> Data source origin of the feature.</div>
747
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
748
+ </div>
749
+ </p>
750
+ <p>
751
+ <h5 id="objectPropertydbxref">Object Property gfvo:dbxref</h5>
752
+ <div style="margin-left: 16px; margin-bottom: 16px">
753
+ <div><i>Domain:</i> <a href="#classDataSource">DataSource</a>, <a href="#classFeature">Feature</a>, <a href="#classMethod">Method</a>, <a href="#classPhenotypeDescription">PhenotypeDescription</a>, <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
754
+ <div><i>Range:</i> <a href="http://www.w3.org/2002/07/owl#Thing">http://www.w3.org/2002/07/owl#Thing</a></div>
755
+ <div><i>Label:</i> dbxref</div>
756
+ <div><i>Comment:</i> A database cross-reference to associate a feature or its structured pragma metadata in GVF to a representation in another database.</div>
757
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
758
+ </div>
759
+ </p>
760
+ <p>
761
+ <h5 id="objectPropertyeffect">Object Property gfvo:effect</h5>
762
+ <div style="margin-left: 16px; margin-bottom: 16px">
763
+ <div><i>Domain:</i> <a href="#classVariant">Variant</a></div>
764
+ <div><i>Range:</i> <a href="#classEffect">Effect</a></div>
765
+ <div><i>Label:</i> effect</div>
766
+ <div><i>Comment:</i> An effect of a particular feature variant.</div>
767
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
768
+ </div>
769
+ </p>
770
+ <p>
771
+ <h5 id="objectPropertyeffectObjectProperty">Object Property gfvo:effectObjectProperty</h5>
772
+ <div style="margin-left: 16px; margin-bottom: 16px">
773
+ <div><i>Label:</i> effect object property</div>
774
+ <div><i>Comment:</i> Properties that are directly associated with <a href="#classEffect">Effect</a> class instances.</div>
775
+ <div></div>
776
+ </div>
777
+ </p>
778
+ <p>
779
+ <h5 id="objectPropertyfeatureAnnotationObjectProperty">Object Property gfvo:featureAnnotationObjectProperty</h5>
780
+ <div style="margin-left: 16px; margin-bottom: 16px">
781
+ <div><i>Label:</i> feature annotation object property</div>
782
+ <div><i>Comment:</i> Property of one of the genomic annotation classes, such as <a href="#classBreakpoint">Breakpoint</a>, <a href="#classReference">Reference</a>, <a href="#classVariant">Variant</a>. For properties related to the core genomic data class <a href="#classFeature">Feature</a>, see <a href="#datatypePropertyfeatureDatatypeProperty">feature datatype property</a> or <a href="#objectPropertyfeatureObjectProperty">feature object property</a>.</div>
783
+ <div></div>
784
+ </div>
785
+ </p>
786
+ <p>
787
+ <h5 id="objectPropertyfeatureObjectProperty">Object Property gfvo:featureObjectProperty</h5>
788
+ <div style="margin-left: 16px; margin-bottom: 16px">
789
+ <div><i>Label:</i> feature object property</div>
790
+ <div><i>Comment:</i> Properties that are directly associated with <a href="#classFeature">Feature</a> class instances. For properties related to <a href="#classReference">Reference</a>, <a href="#classVariant">Variant</a>, or other genomic annotation classes, see <a href="#datatypePropertyfeatureAnnotationDatatypeProperty">feature annotation datatype property</a> or <a href="#objectPropertyfeatureAnnotationObjectProperty">feature annotation object property</a>.</div>
791
+ <div></div>
792
+ </div>
793
+ </p>
794
+ <p>
795
+ <h5 id="objectPropertyfeatureOntology">Object Property gfvo:featureOntology</h5>
796
+ <div style="margin-left: 16px; margin-bottom: 16px">
797
+ <div><i>Domain:</i> <a href="#classSet">Set</a></div>
798
+ <div><i>Range:</i> <a href="http://www.w3.org/2002/07/owl#Thing">http://www.w3.org/2002/07/owl#Thing</a></div>
799
+ <div><i>Label:</i> feature ontology</div>
800
+ <div><i>Comment:</i> Explicit link-out to one or more ontologies that have been used for describing features. This is a meta comment about the URIs that link out to SO/SOFA or other ontologies.</div>
801
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
802
+ </div>
803
+ </p>
804
+ <p>
805
+ <h5 id="objectPropertyfeatureType">Object Property gfvo:featureType</h5>
806
+ <div style="margin-left: 16px; margin-bottom: 16px">
807
+ <div><i>Domain:</i> <a href="#classEffect">Effect</a></div>
808
+ <div><i>Range:</i> <a href="http://www.w3.org/2002/07/owl#Thing">http://www.w3.org/2002/07/owl#Thing</a></div>
809
+ <div><i>Label:</i> feature type</div>
810
+ <div><i>Comment:</i> A term that is describing the sequence feature that is being affected.</div>
811
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
812
+ </div>
813
+ </p>
814
+ <p>
815
+ <h5 id="objectPropertygenomicSource">Object Property gfvo:genomicSource</h5>
816
+ <div style="margin-left: 16px; margin-bottom: 16px">
817
+ <div><i>Domain:</i> <a href="#classSet">Set</a></div>
818
+ <div><i>Range:</i> <a href="http://www.w3.org/2002/07/owl#Thing">http://www.w3.org/2002/07/owl#Thing</a></div>
819
+ <div><i>Label:</i> genomic source</div>
820
+ <div><i>Comment:</i> Denotes the source of genomic data (on a cell-type level). Valid object assignments are individuals of the &quot;Genomic Source&quot; enumeration class.</div>
821
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
822
+ </div>
823
+ </p>
824
+ <p>
825
+ <h5 id="objectPropertygenotype">Object Property gfvo:genotype</h5>
826
+ <div style="margin-left: 16px; margin-bottom: 16px">
827
+ <div><i>Domain:</i> <a href="#classVariant">Variant</a></div>
828
+ <div><i>Range:</i> <a href="#classChromosome">Chromosome</a></div>
829
+ <div><i>Label:</i> genotype</div>
830
+ <div><i>Comment:</i> Determines the genotype as observed in an individual.</div>
831
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
832
+ </div>
833
+ </p>
834
+ <p>
835
+ <h5 id="objectPropertyindividual">Object Property gfvo:individual</h5>
836
+ <div style="margin-left: 16px; margin-bottom: 16px">
837
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
838
+ <div><i>Range:</i> <a href="#classSequencedIndividual">SequencedIndividual</a></div>
839
+ <div><i>Label:</i> individual</div>
840
+ <div><i>Comment:</i> Links to information about an individual.</div>
841
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
842
+ </div>
843
+ </p>
844
+ <p>
845
+ <h5 id="objectPropertylocus">Object Property gfvo:locus</h5>
846
+ <div style="margin-left: 16px; margin-bottom: 16px">
847
+ <div><i>Domain:</i> <a href="#classBreakpoint">Breakpoint</a>, <a href="#classEffect">Effect</a>, <a href="#classFeature">Feature</a>, <a href="#classLandmark">Landmark</a>, <a href="#classTarget">Target</a></div>
848
+ <div><i>Range:</i> <a href="http://biohackathon.org/resource/faldo#Region">http://biohackathon.org/resource/faldo#Region</a></div>
849
+ <div><i>Label:</i> locus</div>
850
+ <div><i>Comment:</i> The locus determines the genomic position of an genomic object. The FALDO &quot;Region&quot; class can denote genomic feature&apos;s start, stop, and strand properties, it can express fuzzy genomic ranges if exact genomic coordinates are unknown. For <a href="#classLandmark">Landmark</a> class instances, the locus provides the start and end coordinates of the landmark.</div>
851
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
852
+ </div>
853
+ </p>
854
+ <p>
855
+ <h5 id="objectPropertylocusAnnotationObjectProperty">Object Property gfvo:locusAnnotationObjectProperty</h5>
856
+ <div style="margin-left: 16px; margin-bottom: 16px">
857
+ <div><i>Label:</i> locus annotation object property</div>
858
+ <div><i>Comment:</i> A property related to genomic coordinates. This can be a <a href="#objectPropertylocus">locus</a> description that uses FALDO to denote Regions (with exact or probabilistic/fuzzy boundaries; <a href="#classBreakpoint">Breakpoint</a> locations) or an &quot;operation&quot; of a list of <a href="#classAlignmentOperation">Alignment Operation</a> instances that encode a CIGAR line.</div>
859
+ <div></div>
860
+ </div>
861
+ </p>
862
+ <p>
863
+ <h5 id="objectPropertyontologyTerm">Object Property gfvo:ontologyTerm</h5>
864
+ <div style="margin-left: 16px; margin-bottom: 16px">
865
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a>, <a href="#classVariant">Variant</a></div>
866
+ <div><i>Range:</i> <a href="http://www.w3.org/2002/07/owl#Thing">http://www.w3.org/2002/07/owl#Thing</a></div>
867
+ <div><i>Label:</i> ontology term</div>
868
+ <div><i>Comment:</i> A cross-reference to an ontology term that is associated with a feature. For instances of the <a href="#classVariant">Variant</a> class, the associated ontology term must be a Variant Ontology term (VariO; http://purl.obolibrary.org/obo/VariO_0001 or subclasses thereof).</div>
869
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
870
+ </div>
871
+ </p>
872
+ <p>
873
+ <h5 id="objectPropertyparent">Object Property gfvo:parent</h5>
874
+ <div style="margin-left: 16px; margin-bottom: 16px">
875
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
876
+ <div><i>Range:</i> <a href="#classFeature">Feature</a></div>
877
+ <div><i>Label:</i> parent</div>
878
+ <div><i>Comment:</i> Link out to a parent feature.</div>
879
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
880
+ </div>
881
+ </p>
882
+ <p>
883
+ <h5 id="objectPropertyphenotypeDescription">Object Property gfvo:phenotypeDescription</h5>
884
+ <div style="margin-left: 16px; margin-bottom: 16px">
885
+ <div><i>Domain:</i> <a href="#classSet">Set</a></div>
886
+ <div><i>Range:</i> <a href="#classPhenotypeDescription">PhenotypeDescription</a></div>
887
+ <div><i>Label:</i> phenotype description</div>
888
+ <div><i>Comment:</i> Further information about an individual&apos;s phenotype. Applies only to single individual sets.</div>
889
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
890
+ </div>
891
+ </p>
892
+ <p>
893
+ <h5 id="objectPropertyphenotypeDescriptionObjectProperty">Object Property gfvo:phenotypeDescriptionObjectProperty</h5>
894
+ <div style="margin-left: 16px; margin-bottom: 16px">
895
+ <div><i>Label:</i> phenotype description object property</div>
896
+ <div><i>Comment:</i> An object property directly associated with <a href="#classPhenotypeDescription">Phenotype Description</a> class instances.</div>
897
+ <div></div>
898
+ </div>
899
+ </p>
900
+ <p>
901
+ <h5 id="objectPropertyrecordObjectProperty">Object Property gfvo:recordObjectProperty</h5>
902
+ <div style="margin-left: 16px; margin-bottom: 16px">
903
+ <div><i>Label:</i> record object property</div>
904
+ <div><i>Comment:</i> A record object property is directly related to describing genomic feature or variant data. Classes that make use of record object properties are <a href="#classFeature">Feature</a>, <a href="#classVariant">Variant</a>, and so on. For container classes, such as <a href="#classSet">Set</a> and <a href="#classFile">File</a>, see <a href="#objectPropertysetObjectProperty">set object property</a>.</div>
905
+ <div></div>
906
+ </div>
907
+ </p>
908
+ <p>
909
+ <h5 id="objectPropertyreference">Object Property gfvo:reference</h5>
910
+ <div style="margin-left: 16px; margin-bottom: 16px">
911
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
912
+ <div><i>Range:</i> <a href="#classReference">Reference</a></div>
913
+ <div><i>Label:</i> reference</div>
914
+ <div><i>Comment:</i> Specific information about the reference sequence of a feature.</div>
915
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
916
+ </div>
917
+ </p>
918
+ <p>
919
+ <h5 id="objectPropertyscoreMethod">Object Property gfvo:scoreMethod</h5>
920
+ <div style="margin-left: 16px; margin-bottom: 16px">
921
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
922
+ <div><i>Range:</i> <a href="#classMethod">Method</a></div>
923
+ <div><i>Label:</i> score method</div>
924
+ <div><i>Comment:</i> Used scoring method, which is described in more detail by a <a href="#classMethod">Method</a> class instance.</div>
925
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
926
+ </div>
927
+ </p>
928
+ <p>
929
+ <h5 id="objectPropertyseqid">Object Property gfvo:seqid</h5>
930
+ <div style="margin-left: 16px; margin-bottom: 16px">
931
+ <div><i>Domain:</i> <a href="#classBreakpoint">Breakpoint</a>, <a href="#classFeature">Feature</a></div>
932
+ <div><i>Range:</i> <a href="#classLandmark">Landmark</a></div>
933
+ <div><i>Label:</i> seqid</div>
934
+ <div><i>Comment:</i> Establishes the landmark on which the feature or breakpoint is located. A landmark is typically a chromosome, scaffold or contig, but can be any other genomic object (DNA, RNA, protein) in principle.</div>
935
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
936
+ </div>
937
+ </p>
938
+ <p>
939
+ <h5 id="objectPropertysequenceVariant">Object Property gfvo:sequenceVariant</h5>
940
+ <div style="margin-left: 16px; margin-bottom: 16px">
941
+ <div><i>Domain:</i> <a href="#classEffect">Effect</a></div>
942
+ <div><i>Range:</i> <a href="http://www.w3.org/2002/07/owl#Thing">http://www.w3.org/2002/07/owl#Thing</a></div>
943
+ <div><i>Label:</i> sequence variant</div>
944
+ <div><i>Comment:</i> Effect of a sequence alteration on a sequence feature.</div>
945
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
946
+ </div>
947
+ </p>
948
+ <p>
949
+ <h5 id="objectPropertysequencedIndividualObjectProperty">Object Property gfvo:sequencedIndividualObjectProperty</h5>
950
+ <div style="margin-left: 16px; margin-bottom: 16px">
951
+ <div><i>Label:</i> sequenced individual object property</div>
952
+ <div><i>Comment:</i> A property that is directly associated with <a href="#classSequencedIndividual">Sequenced Individual</a> class instances.</div>
953
+ <div></div>
954
+ </div>
955
+ </p>
956
+ <p>
957
+ <h5 id="objectPropertysetAnnotationObjectProperty">Object Property gfvo:setAnnotationObjectProperty</h5>
958
+ <div style="margin-left: 16px; margin-bottom: 16px">
959
+ <div><i>Label:</i> set annotation object property</div>
960
+ <div><i>Comment:</i> A property related to the annotation of <a href="#classSet">Set</a> class instances or its sub-classes, s.a. <a href="#classPhenotypeDescription">Phenotype Description</a>.</div>
961
+ <div></div>
962
+ </div>
963
+ </p>
964
+ <p>
965
+ <h5 id="objectPropertysetObjectProperty">Object Property gfvo:setObjectProperty</h5>
966
+ <div style="margin-left: 16px; margin-bottom: 16px">
967
+ <div><i>Label:</i> set object property</div>
968
+ <div><i>Comment:</i> A property that is directly associated with the <a href="#classSet">Set</a> class. Immediate sub-properties of this property are independent to specific specifications such as GFF3, GTF, GVF or VCF. Not all sub-properties can be preserved when carrying out operations between multiple <a href="#classSet">Set</a> class instances. For example, the &quot;sex&quot; property applies to single individual sets and can only be kept in a set union between multiple <a href="#classSet">Set</a> class instances if all involved instances agree on this property. For genomic feature and variant related properties, see <a href="#objectPropertyrecordObjectProperty">record object property</a> and <a href="#datatypePropertyrecordDatatypeProperty">record datatype property</a>.</div>
969
+ <div></div>
970
+ </div>
971
+ </p>
972
+ <p>
973
+ <h5 id="objectPropertysourceMethod">Object Property gfvo:sourceMethod</h5>
974
+ <div style="margin-left: 16px; margin-bottom: 16px">
975
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
976
+ <div><i>Range:</i> <a href="#classMethod">Method</a></div>
977
+ <div><i>Label:</i> source method</div>
978
+ <div><i>Comment:</i> Further information about the algorithm/methodologies used.</div>
979
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
980
+ </div>
981
+ </p>
982
+ <p>
983
+ <h5 id="objectPropertyspecies">Object Property gfvo:species</h5>
984
+ <div style="margin-left: 16px; margin-bottom: 16px">
985
+ <div><i>Domain:</i> <a href="#classSet">Set</a></div>
986
+ <div><i>Range:</i> <a href="http://purl.obolibrary.org/obo/NCBITaxon_1">http://purl.obolibrary.org/obo/NCBITaxon_1</a></div>
987
+ <div><i>Label:</i> species</div>
988
+ <div><i>Comment:</i> NCBI Taxonomy Ontology &quot;NCBITaxon_1&quot; (or sub-classes) instance that denotes the species for a feature set.</div>
989
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
990
+ </div>
991
+ </p>
992
+ <p>
993
+ <h5 id="objectPropertystructuredAttributes">Object Property gfvo:structuredAttributes</h5>
994
+ <div style="margin-left: 16px; margin-bottom: 16px">
995
+ <div><i>Domain:</i> <a href="#classStructuredAttribute">StructuredAttribute</a></div>
996
+ <div><i>Label:</i> structured attributes</div>
997
+ <div><i>Comment:</i> Tag name/value pair attributes that are not captured by the GVF specification.</div>
998
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
999
+ </div>
1000
+ </p>
1001
+ <p>
1002
+ <h5 id="objectPropertytarget">Object Property gfvo:target</h5>
1003
+ <div style="margin-left: 16px; margin-bottom: 16px">
1004
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
1005
+ <div><i>Range:</i> <a href="#classTarget">Target</a></div>
1006
+ <div><i>Label:</i> target</div>
1007
+ <div><i>Comment:</i> Identifies the target that the features aligns to.</div>
1008
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1009
+ </div>
1010
+ </p>
1011
+ <p>
1012
+ <h5 id="objectPropertytargetAttributeMethod">Object Property gfvo:targetAttributeMethod</h5>
1013
+ <div style="margin-left: 16px; margin-bottom: 16px">
1014
+ <div><i>Domain:</i> <a href="#classTarget">Target</a></div>
1015
+ <div><i>Range:</i> <a href="#classMethod">Method</a></div>
1016
+ <div><i>Label:</i> target attribute method</div>
1017
+ <div><i>Comment:</i> Further information about the associated attribute(s).</div>
1018
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1019
+ </div>
1020
+ </p>
1021
+ <p>
1022
+ <h5 id="objectPropertytargetProperty">Object Property gfvo:targetProperty</h5>
1023
+ <div style="margin-left: 16px; margin-bottom: 16px">
1024
+ <div><i>Label:</i> target property</div>
1025
+ <div><i>Comment:</i> A properties that is directly associated with <a href="#classTarget">Target</a> class instances.</div>
1026
+ <div></div>
1027
+ </div>
1028
+ </p>
1029
+ <p>
1030
+ <h5 id="objectPropertytechnologicalAnnotationObjectProperty">Object Property gfvo:technologicalAnnotationObjectProperty</h5>
1031
+ <div style="margin-left: 16px; margin-bottom: 16px">
1032
+ <div><i>Label:</i> technological annotation object property</div>
1033
+ <div><i>Comment:</i> An object property associated with annotations that are related to technological aspects regarding a genomic feature or variant. For example, a property of a <a href="#classTechnologyPlatform">Technology Platform</a> or <a href="#classDataSource">Data Source</a>.</div>
1034
+ <div></div>
1035
+ </div>
1036
+ </p>
1037
+ <p>
1038
+ <h5 id="objectPropertytechnologyPlatform">Object Property gfvo:technologyPlatform</h5>
1039
+ <div style="margin-left: 16px; margin-bottom: 16px">
1040
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
1041
+ <div><i>Range:</i> <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
1042
+ <div><i>Label:</i> technology platform</div>
1043
+ <div><i>Comment:</i> Technology platform that was used to derive the feature.</div>
1044
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1045
+ </div>
1046
+ </p>
1047
+ <p>
1048
+ <h5 id="objectPropertytype">Object Property gfvo:type</h5>
1049
+ <div style="margin-left: 16px; margin-bottom: 16px">
1050
+ <div><i>Domain:</i> <a href="#classFile">File</a></div>
1051
+ <div><i>Range:</i> <a href="http://www.sequenceontology.org/miso/current_release/term/SO:0000110">http://www.sequenceontology.org/miso/current_release/term/SO:0000110</a></div>
1052
+ <div><i>Label:</i> type</div>
1053
+ <div><i>Comment:</i> Type of the feature, which is a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO).</div>
1054
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1055
+ </div>
1056
+ </p>
1057
+ <p>
1058
+ <h5 id="objectPropertyvariant">Object Property gfvo:variant</h5>
1059
+ <div style="margin-left: 16px; margin-bottom: 16px">
1060
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
1061
+ <div><i>Range:</i> <a href="#classVariant">Variant</a></div>
1062
+ <div><i>Label:</i> variant</div>
1063
+ <div><i>Comment:</i> Specific information about the variant(s) of a feature.</div>
1064
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
1065
+ </div>
1066
+ </p>
1067
+ <p>
1068
+ <h5 id="objectPropertyvariantObjectProperty">Object Property gfvo:variantObjectProperty</h5>
1069
+ <div style="margin-left: 16px; margin-bottom: 16px">
1070
+ <div><i>Label:</i> variant object property</div>
1071
+ <div><i>Comment:</i> Properties that are directly associated with <a href="#classVariant">Variant</a> class instances.</div>
1072
+ <div></div>
1073
+ </div>
1074
+ </p>
1075
+ <p>
1076
+ <h5 id="objectPropertyvariationAnnotationObjectProperty">Object Property gfvo:variationAnnotationObjectProperty</h5>
1077
+ <div style="margin-left: 16px; margin-bottom: 16px">
1078
+ <div><i>Label:</i> variation annotation object property</div>
1079
+ <div><i>Comment:</i> A variation annotation object property is describing an object property of a <a href="#classVariant">Variant</a> or <a href="#classEffect">Effect</a> class instance.</div>
1080
+ <div></div>
1081
+ </div>
1082
+ </p>
1083
+ <h4>Datatype Properties (Strings, Numbers, Dates, etc.)</h4>
1084
+ <p>
1085
+ <h5 id="datatypeProperty3primeContext">Datatype Property gfvo:3primeContext</h5>
1086
+ <div style="margin-left: 16px; margin-bottom: 16px">
1087
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
1088
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1089
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1090
+ <div><i>Label:</i> 3&apos; context</div>
1091
+ <div><i>Comment:</i> Sequence context of a feature on the positive strand (forward strand) on the 3&apos; end. A valid sequence context is denoted by a string of one or more concatenated letters A, C, G, or T.</div>
1092
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1093
+ </div>
1094
+ </p>
1095
+ <p>
1096
+ <h5 id="datatypeProperty5primeContext">Datatype Property gfvo:5primeContext</h5>
1097
+ <div style="margin-left: 16px; margin-bottom: 16px">
1098
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
1099
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1100
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1101
+ <div><i>Label:</i> 5&apos; context</div>
1102
+ <div><i>Comment:</i> Sequence context of a feature on the positive strand (forward strand) on the 5&apos; end. A valid sequence context is denoted by a string of one or more concatenated letters A, C, G, or T.</div>
1103
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1104
+ </div>
1105
+ </p>
1106
+ <p>
1107
+ <h5 id="datatypePropertyalias">Datatype Property gfvo:alias</h5>
1108
+ <div style="margin-left: 16px; margin-bottom: 16px">
1109
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
1110
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1111
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1112
+ <div><i>Label:</i> alias</div>
1113
+ <div><i>Comment:</i> Secondary name of a feature besides the primary feature ID. The secondary name can be a HGVS/ISCN nomenclature name, but not a cross-reference to a database (e.g. dbSNP, OMIM). Cross-references should be made using the <a href="#objectPropertydbxref">dbxref</a> property.</div>
1114
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1115
+ </div>
1116
+ </p>
1117
+ <p>
1118
+ <h5 id="datatypePropertyalignmentOperationDatatypeProperty">Datatype Property gfvo:alignmentOperationDatatypeProperty</h5>
1119
+ <div style="margin-left: 16px; margin-bottom: 16px">
1120
+ <div><i>Label:</i> alignment operation datatype property</div>
1121
+ <div><i>Comment:</i> Property that is directly associated with <a href="#classAlignmentOperation">Alignment Operation</a> instances.</div>
1122
+ <div></div>
1123
+ </div>
1124
+ </p>
1125
+ <p>
1126
+ <h5 id="datatypePropertyaminoAcid">Datatype Property gfvo:aminoAcid</h5>
1127
+ <div style="margin-left: 16px; margin-bottom: 16px">
1128
+ <div><i>Domain:</i> <a href="#classReference">Reference</a>, <a href="#classVariant">Variant</a></div>
1129
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1130
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1131
+ <div><i>Label:</i> amino acid</div>
1132
+ <div><i>Comment:</i> Amino acid in the reference genome that overlaps with a variant&apos;s genome coordinates.</div>
1133
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
1134
+ </div>
1135
+ </p>
1136
+ <p>
1137
+ <h5 id="datatypePropertyaverageCoverage">Datatype Property gfvo:averageCoverage</h5>
1138
+ <div style="margin-left: 16px; margin-bottom: 16px">
1139
+ <div><i>Domain:</i> <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
1140
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#int">http://www.w3.org/2001/XMLSchema#int</a></div>
1141
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1142
+ <div><i>Label:</i> average coverage</div>
1143
+ <div><i>Comment:</i> Undocumented in GVF specification. Even though the property&apos;s semantics are undocumented, it is still included in the ontology in order to reflect the data values that might be encoded in GVF files.</div>
1144
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1145
+ </div>
1146
+ </p>
1147
+ <p>
1148
+ <h5 id="datatypePropertybuild">Datatype Property gfvo:build</h5>
1149
+ <div style="margin-left: 16px; margin-bottom: 16px">
1150
+ <div><i>Domain:</i> <a href="#classSet">Set</a></div>
1151
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1152
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1153
+ <div><i>Label:</i> build</div>
1154
+ <div><i>Comment:</i> Name of a genome assembly build that denotes the provenance of genomic features and variants in a <a href="#classSet">Set</a>. For example, &apos;GRCh37&apos;, &apos;NCBI 36&apos;, &apos;FlyBase r4.1&apos;, or &apos;hg19&apos;. If possible, the patch level of the assembly build should be included, such as &apos;GRCh37.p7&apos;.</div>
1155
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1156
+ </div>
1157
+ </p>
1158
+ <p>
1159
+ <h5 id="datatypePropertycodon">Datatype Property gfvo:codon</h5>
1160
+ <div style="margin-left: 16px; margin-bottom: 16px">
1161
+ <div><i>Domain:</i> <a href="#classReference">Reference</a>, <a href="#classVariant">Variant</a></div>
1162
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1163
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1164
+ <div><i>Label:</i> codon</div>
1165
+ <div><i>Comment:</i> Describes the codon from the reference sequence whose coordinates overlap with this variant. A valid codon description is a string of three -- or multiples thereof -- concatenated letters A, C, G, or T.</div>
1166
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1167
+ </div>
1168
+ </p>
1169
+ <p>
1170
+ <h5 id="datatypePropertycomment">Datatype Property gfvo:comment</h5>
1171
+ <div style="margin-left: 16px; margin-bottom: 16px">
1172
+ <div><i>Domain:</i> <a href="#classDataSource">DataSource</a>, <a href="#classMethod">Method</a>, <a href="#classPhenotypeDescription">PhenotypeDescription</a>, <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
1173
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1174
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1175
+ <div><i>Label:</i> comment</div>
1176
+ <div><i>Comment:</i> Comments should be made using &quot;http://www.w3.org/2000/01/rdf-schema#comment&quot;.This datatype property only exists to redirect the focus to RDF Schema for commenting, since it might be expected that comments are modeled similar to other datatype properties involving <a href="#classDataSource">Data Source</a>, <a href="#classMethod">Method</a>, <a href="#classPhenotypeDescription">Phenotype Description</a> or <a href="#classTechnologyPlatform">Technology Platform</a>.</div>
1177
+ <div></div>
1178
+ </div>
1179
+ </p>
1180
+ <p>
1181
+ <h5 id="datatypePropertycustomAnnotationDatatypeProperty">Datatype Property gfvo:customAnnotationDatatypeProperty</h5>
1182
+ <div style="margin-left: 16px; margin-bottom: 16px">
1183
+ <div><i>Label:</i> custom annotation datatype property</div>
1184
+ <div><i>Comment:</i> Datatype property of an <a href="#classAttribute">Attribute</a> or <a href="#classStructuredAttribute">Structured Attribute</a> class instance. <a href="#classAttribute">Attribute</a> and <a href="#classStructuredAttribute">Structured Attribute</a> class instances are used to capture genomic feature and variation data assignments that may appear in a GFF3, GTF, GVF or VCF file, but which are not covered by their respective specifications.</div>
1185
+ <div></div>
1186
+ </div>
1187
+ </p>
1188
+ <p>
1189
+ <h5 id="datatypePropertyeffectDatatypeProperty">Datatype Property gfvo:effectDatatypeProperty</h5>
1190
+ <div style="margin-left: 16px; margin-bottom: 16px">
1191
+ <div><i>Label:</i> effect datatype property</div>
1192
+ <div><i>Comment:</i> A datatype property that are directly associated with <a href="#classEffect">Effect</a> class instances.</div>
1193
+ <div></div>
1194
+ </div>
1195
+ </p>
1196
+ <p>
1197
+ <h5 id="datatypePropertyfeature">Datatype Property gfvo:feature</h5>
1198
+ <div style="margin-left: 16px; margin-bottom: 16px">
1199
+ <div><i>Domain:</i> <a href="#classEffect">Effect</a></div>
1200
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1201
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1202
+ <div><i>Label:</i> feature</div>
1203
+ <div><i>Comment:</i> Features that are affected by this sequence alteration effect. This can be an external feature identifier, such as an Ensembl gene/transcript identifier.</div>
1204
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1205
+ </div>
1206
+ </p>
1207
+ <p>
1208
+ <h5 id="datatypePropertyfeatureAnnotationDatatypeProperty">Datatype Property gfvo:featureAnnotationDatatypeProperty</h5>
1209
+ <div style="margin-left: 16px; margin-bottom: 16px">
1210
+ <div><i>Label:</i> feature annotation datatype property</div>
1211
+ <div><i>Comment:</i> Property of one of the genomic annotation classes, such as <a href="#classBreakpoint">Breakpoint</a>, <a href="#classReference">Reference</a>, <a href="#classVariant">Variant</a>. For properties related to the core genomic data class <a href="#classFeature">Feature</a>, see <a href="#datatypePropertyfeatureDatatypeProperty">feature datatype property</a> or <a href="#objectPropertyfeatureObjectProperty">feature object property</a>.</div>
1212
+ <div></div>
1213
+ </div>
1214
+ </p>
1215
+ <p>
1216
+ <h5 id="datatypePropertyfeatureDatatypeProperty">Datatype Property gfvo:featureDatatypeProperty</h5>
1217
+ <div style="margin-left: 16px; margin-bottom: 16px">
1218
+ <div><i>Label:</i> feature datatype property</div>
1219
+ <div><i>Comment:</i> Property that is directly associated with a <a href="#classFeature">Feature</a> class instance. For properties related to <a href="#classReference">Reference</a>, <a href="#classVariant">Variant</a>, or other genomic annotation classes, see <a href="#datatypePropertyfeatureAnnotationDatatypeProperty">feature annotation datatype property</a> or <a href="#objectPropertyfeatureAnnotationObjectProperty">feature annotation object property</a>.</div>
1220
+ <div></div>
1221
+ </div>
1222
+ </p>
1223
+ <p>
1224
+ <h5 id="datatypePropertyfileDatatypeProperty">Datatype Property gfvo:fileDatatypeProperty</h5>
1225
+ <div style="margin-left: 16px; margin-bottom: 16px">
1226
+ <div><i>Label:</i> file datatype property</div>
1227
+ <div><i>Comment:</i> Datatype properties related to <a href="#classFile">File</a> class instances. Subclasses of this property are used for denoting data that is specific to files only and which is only preserved as a means to encode for all data items defined by the GFF3, GTF, GVF and VCF specifications. These properties cannot be carried over into the result of set operations (s.a. union) between <a href="#classFile">File</a>/<a href="#classSet">Set</a> class instances. Keeping these properties in the result set between set operations may result in wrong annotations or contradictions (e.g., mutliple assignment of different versions or dates).</div>
1228
+ <div></div>
1229
+ </div>
1230
+ </p>
1231
+ <p>
1232
+ <h5 id="datatypePropertyfileDate">Datatype Property gfvo:fileDate</h5>
1233
+ <div style="margin-left: 16px; margin-bottom: 16px">
1234
+ <div><i>Domain:</i> <a href="#classFile">File</a></div>
1235
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#dateTime">http://www.w3.org/2001/XMLSchema#dateTime</a></div>
1236
+ <div><i>Label:</i> file date</div>
1237
+ <div><i>Comment:</i> Creation date of the data file whose genomic data is captured by the associated <a href="#classFile">File</a> instance.</div>
1238
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1239
+ </div>
1240
+ </p>
1241
+ <p>
1242
+ <h5 id="datatypePropertyfileVersion">Datatype Property gfvo:fileVersion</h5>
1243
+ <div style="margin-left: 16px; margin-bottom: 16px">
1244
+ <div><i>Domain:</i> <a href="#classFile">File</a></div>
1245
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1246
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1247
+ <div><i>Label:</i> file version</div>
1248
+ <div><i>Comment:</i> Proprietary version of the file or its contents whose genomic data is associated with a <a href="#classFile">File</a> instance.</div>
1249
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1250
+ </div>
1251
+ </p>
1252
+ <p>
1253
+ <h5 id="datatypePropertyfrequency">Datatype Property gfvo:frequency</h5>
1254
+ <div style="margin-left: 16px; margin-bottom: 16px">
1255
+ <div><i>Domain:</i> <a href="#classVariant">Variant</a></div>
1256
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#float">http://www.w3.org/2001/XMLSchema#float</a></div>
1257
+ <div><i>Label:</i> frequency</div>
1258
+ <div><i>Comment:</i> Frequency of a variant in a population. The population is determined by the <a href="#classSet">Set</a> in which the <a href="#classVariant">Variant</a> resides.</div>
1259
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1260
+ </div>
1261
+ </p>
1262
+ <p>
1263
+ <h5 id="datatypePropertygffVersion">Datatype Property gfvo:gffVersion</h5>
1264
+ <div style="margin-left: 16px; margin-bottom: 16px">
1265
+ <div><i>Domain:</i> <a href="#classFile">File</a></div>
1266
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#float">http://www.w3.org/2001/XMLSchema#float</a></div>
1267
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1268
+ <div><i>Label:</i> gff version</div>
1269
+ <div><i>Comment:</i> Version of the GFF3 specification that defines the contents captured by the <a href="#classFile">File</a> class instance. The version number should be greater or equal than 3.0, but less than 4.0. For GFF2/GTF version number assignment, see the <a href="#datatypePropertygtfVersion">gtf version</a> datatype property.</div>
1270
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1271
+ </div>
1272
+ </p>
1273
+ <p>
1274
+ <h5 id="datatypePropertygtfVersion">Datatype Property gfvo:gtfVersion</h5>
1275
+ <div style="margin-left: 16px; margin-bottom: 16px">
1276
+ <div><i>Domain:</i> <a href="#classFile">File</a></div>
1277
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#float">http://www.w3.org/2001/XMLSchema#float</a></div>
1278
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1279
+ <div><i>Label:</i> gtf version</div>
1280
+ <div><i>Comment:</i> Version of the GTF specification that defines the contents captured by the <a href="#classFile">File</a> class instance. The version number should be greater or equal than 2.0, but less than 3.0. This number derives from the fact that GTF files are equivalent to GFF2 files. GTF/GFF2 files are incompatible with the GFF3 specification. For GFF3 version number assignment, see the <a href="#datatypePropertygffVersion">gff version</a> datatype property.</div>
1281
+ <div><span style="margin-right: 4px;" class="badge badge-info">GTF</span></div>
1282
+ </div>
1283
+ </p>
1284
+ <p>
1285
+ <h5 id="datatypePropertygvfVersion">Datatype Property gfvo:gvfVersion</h5>
1286
+ <div style="margin-left: 16px; margin-bottom: 16px">
1287
+ <div><i>Domain:</i> <a href="#classFile">File</a></div>
1288
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#float">http://www.w3.org/2001/XMLSchema#float</a></div>
1289
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1290
+ <div><i>Label:</i> gvf version</div>
1291
+ <div><i>Comment:</i> Version of the GVF specification that defines the contents captured by the <a href="#classFile">File</a> class instance. The version number should be greater or equal than 1.0, but less than 2.0. GVF files usually make a statement about their underlying GFF3 specification that they rely on too, which should be encoded using the <a href="#datatypePropertygffVersion">gff version</a> datatype property.</div>
1292
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1293
+ </div>
1294
+ </p>
1295
+ <p>
1296
+ <h5 id="datatypePropertyid">Datatype Property gfvo:id</h5>
1297
+ <div style="margin-left: 16px; margin-bottom: 16px">
1298
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a>, <a href="#classLandmark">Landmark</a>, <a href="#classTarget">Target</a></div>
1299
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1300
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1301
+ <div><i>Label:</i> id</div>
1302
+ <div><i>Comment:</i> A unique identifier for the feature within the feature set (a <a href="#classSet">Set</a>/<a href="#classFile">File</a> class instance). The unique identifier is important when dealing with GFF3, GTF, GVF or VCF files as a stand in object that makes the aggregation and separation of genomic feature and variant information possible. In RDF, the URI of subject should be used primarily, provided that its URI can be considered stable.</div>
1303
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
1304
+ </div>
1305
+ </p>
1306
+ <p>
1307
+ <h5 id="datatypePropertyisCircular">Datatype Property gfvo:isCircular</h5>
1308
+ <div style="margin-left: 16px; margin-bottom: 16px">
1309
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
1310
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#boolean">http://www.w3.org/2001/XMLSchema#boolean</a></div>
1311
+ <div><i>Label:</i> </div>
1312
+ <div><i>Comment:</i> Truth value describing whether the feature is circular or not. This can be used to describe, for example, circular DNA as being found in bacteria or viruses. It can also be applied to mitochondrial DNA or plastid DNA, where applicable.</div>
1313
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1314
+ </div>
1315
+ </p>
1316
+ <p>
1317
+ <h5 id="datatypePropertyisPhased">Datatype Property gfvo:isPhased</h5>
1318
+ <div style="margin-left: 16px; margin-bottom: 16px">
1319
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a>, <a href="#classVariant">Variant</a></div>
1320
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#boolean">http://www.w3.org/2001/XMLSchema#boolean</a></div>
1321
+ <div><i>Label:</i> is phased</div>
1322
+ <div><i>Comment:</i> Indicates whether this particular feature is phased. Used to encode &quot;##phased-genotypes&quot; statements in GFF3, but can be appropriated freely. It is also a property of GVF variants, even though the GVF specification is unclear on its exact usage details.</div>
1323
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1324
+ </div>
1325
+ </p>
1326
+ <p>
1327
+ <h5 id="datatypePropertylandmarkDatatypeProperty">Datatype Property gfvo:landmarkDatatypeProperty</h5>
1328
+ <div style="margin-left: 16px; margin-bottom: 16px">
1329
+ <div><i>Label:</i> landmark datatype property</div>
1330
+ <div><i>Comment:</i> Property that is directly associated with <a href="#classLandmark">Landmark</a> class instances.</div>
1331
+ <div></div>
1332
+ </div>
1333
+ </p>
1334
+ <p>
1335
+ <h5 id="datatypePropertylocusAnnotationDatatypeProperty">Datatype Property gfvo:locusAnnotationDatatypeProperty</h5>
1336
+ <div style="margin-left: 16px; margin-bottom: 16px">
1337
+ <div><i>Label:</i> locus annotation datatype property</div>
1338
+ <div><i>Comment:</i> A property related to, or associated with, genomic coordinates. This can be a genomic <a href="#datatypePropertysequence">sequence</a> description, the <a href="#datatypePropertyfrequency">frequency</a> of a <a href="#classVariant">Variant</a>, <a href="#datatypePropertyphredScore">phred score</a> of either <a href="#classVariant">Variant</a> or <a href="#classReference">Reference</a>, etc.</div>
1339
+ <div></div>
1340
+ </div>
1341
+ </p>
1342
+ <p>
1343
+ <h5 id="datatypePropertyname">Datatype Property gfvo:name</h5>
1344
+ <div style="margin-left: 16px; margin-bottom: 16px">
1345
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
1346
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1347
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1348
+ <div><i>Label:</i> name</div>
1349
+ <div><i>Comment:</i> Name of a feature, which can be used for display purposes. The name is not a unique property among features in a <a href="#classSet">Set</a>.</div>
1350
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1351
+ </div>
1352
+ </p>
1353
+ <p>
1354
+ <h5 id="datatypePropertynote">Datatype Property gfvo:note</h5>
1355
+ <div style="margin-left: 16px; margin-bottom: 16px">
1356
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
1357
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1358
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1359
+ <div><i>Label:</i> note</div>
1360
+ <div><i>Comment:</i> Free text notes should be made using &quot;http://www.w3.org/2000/01/rdf-schema#comment&quot;.This datatype property only exists to redirect the focus to RDF Schema for annotating features with notes, since it might be expected that a note is similarly modeled to other datatype properties of the <a href="#classFeature">Feature</a> class.</div>
1361
+ <div></div>
1362
+ </div>
1363
+ </p>
1364
+ <p>
1365
+ <h5 id="datatypePropertyphase">Datatype Property gfvo:phase</h5>
1366
+ <div style="margin-left: 16px; margin-bottom: 16px">
1367
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
1368
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#int">http://www.w3.org/2001/XMLSchema#int</a></div>
1369
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1370
+ <div><i>Label:</i> phase</div>
1371
+ <div><i>Comment:</i> Phase of the feature, if it is a CDS. Called &quot;frame&quot; in GTF. A feature&apos;s phase can be either 0, 1, or 2.</div>
1372
+ <div><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1373
+ </div>
1374
+ </p>
1375
+ <p>
1376
+ <h5 id="datatypePropertyphredScore">Datatype Property gfvo:phredScore</h5>
1377
+ <div style="margin-left: 16px; margin-bottom: 16px">
1378
+ <div><i>Domain:</i> <a href="#classReference">Reference</a>, <a href="#classVariant">Variant</a></div>
1379
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#double">http://www.w3.org/2001/XMLSchema#double</a></div>
1380
+ <div><i>Label:</i> phred score</div>
1381
+ <div><i>Comment:</i> A phred-scaled quality score for the reference seuence; -10log_10 prob(no variant). A phred-scaled quality score for a variant sequence; -10log_10 prob(variant call is wrong). High scores indicate high confidence calls. This is a property associated with VCF data. E-values and P-values of features should be expressed using the <a href="#datatypePropertyscore">score</a> datatype property.</div>
1382
+ <div><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
1383
+ </div>
1384
+ </p>
1385
+ <p>
1386
+ <h5 id="datatypePropertyplatformClass">Datatype Property gfvo:platformClass</h5>
1387
+ <div style="margin-left: 16px; margin-bottom: 16px">
1388
+ <div><i>Domain:</i> <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
1389
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1390
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1391
+ <div><i>Label:</i> platform class</div>
1392
+ <div><i>Comment:</i> Type of technology used to gather the variant data. The GVF specification&apos;s list of available classes is naturally incomplete. The range of this property is therefore unrestricted due to its open specification.</div>
1393
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1394
+ </div>
1395
+ </p>
1396
+ <p>
1397
+ <h5 id="datatypePropertyplatformName">Datatype Property gfvo:platformName</h5>
1398
+ <div style="margin-left: 16px; margin-bottom: 16px">
1399
+ <div><i>Domain:</i> <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
1400
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1401
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1402
+ <div><i>Label:</i> platform name</div>
1403
+ <div><i>Comment:</i> Sequencer or other machine used to collect the variant data. The GVF specification&apos;s list of available platforms is naturally incomplete. The range of this property is therefore unrestricted due to its open specification.</div>
1404
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1405
+ </div>
1406
+ </p>
1407
+ <p>
1408
+ <h5 id="datatypePropertyreadIPairSpan">Datatype Property gfvo:readIPairSpan</h5>
1409
+ <div style="margin-left: 16px; margin-bottom: 16px">
1410
+ <div><i>Domain:</i> <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
1411
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#int">http://www.w3.org/2001/XMLSchema#int</a></div>
1412
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1413
+ <div><i>Label:</i> read pair span</div>
1414
+ <div><i>Comment:</i> Undocumented in GVF specification. Even though the property&apos;s semantics are undocumented, it is still included in the ontology in order to reflect the data values that might be encoded in GVF files.</div>
1415
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1416
+ </div>
1417
+ </p>
1418
+ <p>
1419
+ <h5 id="datatypePropertyreadLength">Datatype Property gfvo:readLength</h5>
1420
+ <div style="margin-left: 16px; margin-bottom: 16px">
1421
+ <div><i>Domain:</i> <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
1422
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#int">http://www.w3.org/2001/XMLSchema#int</a></div>
1423
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1424
+ <div><i>Label:</i> read length</div>
1425
+ <div><i>Comment:</i> Undocumented in GVF specification. Even though the property&apos;s semantics are undocumented, it is still included in the ontology in order to reflect the data values that might be encoded in GVF files.</div>
1426
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1427
+ </div>
1428
+ </p>
1429
+ <p>
1430
+ <h5 id="datatypePropertyreads">Datatype Property gfvo:reads</h5>
1431
+ <div style="margin-left: 16px; margin-bottom: 16px">
1432
+ <div><i>Domain:</i> <a href="#classVariant">Variant</a></div>
1433
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#int">http://www.w3.org/2001/XMLSchema#int</a></div>
1434
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1435
+ <div><i>Label:</i> reads</div>
1436
+ <div><i>Comment:</i> Number of reads that are supporting a variant. Valid values are integers greater or equal than zero.</div>
1437
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1438
+ </div>
1439
+ </p>
1440
+ <p>
1441
+ <h5 id="datatypePropertyrecordDatatypeProperty">Datatype Property gfvo:recordDatatypeProperty</h5>
1442
+ <div style="margin-left: 16px; margin-bottom: 16px">
1443
+ <div><i>Label:</i> record datatype property</div>
1444
+ <div><i>Comment:</i> A record datatype property is directly related to describing genomic feature or variant data. Classes that make use of record datatype properties are <a href="#classFeature">Feature</a>, <a href="#classVariant">Variant</a>, and so on. For container classes, such as <a href="#classSet">Set</a> and <a href="#classFile">File</a>, see <a href="#datatypePropertysetDatatypeProperty">set datatype property</a>.</div>
1445
+ <div></div>
1446
+ </div>
1447
+ </p>
1448
+ <p>
1449
+ <h5 id="datatypePropertyreferenceAnnotationDatatypeProperty">Datatype Property gfvo:referenceAnnotationDatatypeProperty</h5>
1450
+ <div style="margin-left: 16px; margin-bottom: 16px">
1451
+ <div><i>Label:</i> reference annotation datatype property</div>
1452
+ <div><i>Comment:</i> Property that is related to a <a href="#classReference">Reference</a> class instance. This property can also be applied to <a href="#classVariant">Variant</a> class instances, which share the same datatype description, but differ in their semantic interpretation of a genomic feature.</div>
1453
+ <div></div>
1454
+ </div>
1455
+ </p>
1456
+ <p>
1457
+ <h5 id="datatypePropertyscore">Datatype Property gfvo:score</h5>
1458
+ <div style="margin-left: 16px; margin-bottom: 16px">
1459
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
1460
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#float">http://www.w3.org/2001/XMLSchema#float</a></div>
1461
+ <div><i>Label:</i> score</div>
1462
+ <div><i>Comment:</i> Score of the feature. For example, an E-value for sequence similarity features or a P-value for ab initio gene prediction features. Phred scores that are associated with reference- or variant-sequences should be encoded using the <a href="#datatypePropertyphredScore">phred score</a> datatype property.</div>
1463
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1464
+ </div>
1465
+ </p>
1466
+ <p>
1467
+ <h5 id="datatypePropertysequence">Datatype Property gfvo:sequence</h5>
1468
+ <div style="margin-left: 16px; margin-bottom: 16px">
1469
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a>, <a href="#classLandmark">Landmark</a>, <a href="#classReference">Reference</a>, <a href="#classVariant">Variant</a></div>
1470
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1471
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1472
+ <div><i>Label:</i> sequence</div>
1473
+ <div><i>Comment:</i> All sequence variations at a locus -- including the reference sequence when appropriate (for example, when the locus is heterozygous). If the feature is on the minus strand, then the sequence is the reverse-compliment of the reference genome for these coordinates.</div>
1474
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1475
+ </div>
1476
+ </p>
1477
+ <p>
1478
+ <h5 id="datatypePropertysequencedIndividualDatatypeProperty">Datatype Property gfvo:sequencedIndividualDatatypeProperty</h5>
1479
+ <div style="margin-left: 16px; margin-bottom: 16px">
1480
+ <div><i>Label:</i> sequenced individual datatype property</div>
1481
+ <div><i>Comment:</i> Property that is directly associated with <a href="#classSequencedIndividual">Sequenced Individual</a> class instances.</div>
1482
+ <div></div>
1483
+ </div>
1484
+ </p>
1485
+ <p>
1486
+ <h5 id="datatypePropertysetDatatypeProperty">Datatype Property gfvo:setDatatypeProperty</h5>
1487
+ <div style="margin-left: 16px; margin-bottom: 16px">
1488
+ <div><i>Label:</i> set datatype property</div>
1489
+ <div><i>Comment:</i> A property that is directly associated with the <a href="#classSet">Set</a> class. Immediate sub-properties of this property are independent to specific specifications such as GFF3, GTF, GVF or VCF. Not all sub-properties can be preserved when carrying out operations between multiple <a href="#classSet">Set</a> class instances. For example, the <a href="#datatypePropertybuild">build</a> property can only be kept in a set union between multiple <a href="#classSet">Set</a> class instances if all involved instances agree on this property. For genomic feature and variant related properties, see <a href="#objectPropertyrecordObjectProperty">record object property</a> and <a href="#datatypePropertyrecordDatatypeProperty">record datatype property</a>.</div>
1490
+ <div></div>
1491
+ </div>
1492
+ </p>
1493
+ <p>
1494
+ <h5 id="datatypePropertysource">Datatype Property gfvo:source</h5>
1495
+ <div style="margin-left: 16px; margin-bottom: 16px">
1496
+ <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
1497
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1498
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1499
+ <div><i>Label:</i> source</div>
1500
+ <div><i>Comment:</i> A free text qualifier that describes the algorithm or operating procedure that generated this feature. For example, the name of the software that generated this feature or a database name.</div>
1501
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1502
+ </div>
1503
+ </p>
1504
+ <p>
1505
+ <h5 id="datatypePropertyspan">Datatype Property gfvo:span</h5>
1506
+ <div style="margin-left: 16px; margin-bottom: 16px">
1507
+ <div><i>Domain:</i> <a href="#classAlignmentOperation">AlignmentOperation</a></div>
1508
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#int">http://www.w3.org/2001/XMLSchema#int</a></div>
1509
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1510
+ <div><i>Label:</i> span</div>
1511
+ <div><i>Comment:</i> A span denotes the number of continuous nucleotides or amino acids an <a href="#classAlignmentOperation">Alignment Operation</a> is annotating. A span can be of length zero or greater.</div>
1512
+ <div></div>
1513
+ </div>
1514
+ </p>
1515
+ <p>
1516
+ <h5 id="datatypePropertytag">Datatype Property gfvo:tag</h5>
1517
+ <div style="margin-left: 16px; margin-bottom: 16px">
1518
+ <div><i>Domain:</i> <a href="#classAttribute">Attribute</a>, <a href="#classStructuredAttribute">StructuredAttribute</a></div>
1519
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
1520
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1521
+ <div><i>Label:</i> tag</div>
1522
+ <div><i>Comment:</i> Tag name of a feature attribute. <a href="#classAttribute">Attribute</a> and <a href="#classStructuredAttribute">Structured Attribute</a> instances are key/value(s) pairs, The key in that assignment is referred to as the <a href="#datatypePropertytag">tag</a>. Custom annotations, i.e. attributes that are not defined by the file format specifications, should use lowercase tags. Future extensions of the specifications might introduce new attributes though, which can be encoded using custom annotations by RDFization tools. The tag should therefore not be treated as strictly lowercase when dealing with custom annotations.</div>
1523
+ <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
1524
+ </div>
1525
+ </p>
1526
+ <p>
1527
+ <h5 id="datatypePropertytargetDatatypeProperty">Datatype Property gfvo:targetDatatypeProperty</h5>
1528
+ <div style="margin-left: 16px; margin-bottom: 16px">
1529
+ <div><i>Label:</i> target datatype property</div>
1530
+ <div><i>Comment:</i> Property that is directly associated with <a href="#classTarget">Target</a> class instances.</div>
1531
+ <div></div>
1532
+ </div>
1533
+ </p>
1534
+ <p>
1535
+ <h5 id="datatypePropertytechnologicalAnnotationDatatypeProperty">Datatype Property gfvo:technologicalAnnotationDatatypeProperty</h5>
1536
+ <div style="margin-left: 16px; margin-bottom: 16px">
1537
+ <div><i>Label:</i> technological annotation datatype property</div>
1538
+ <div><i>Comment:</i> A datatype property associated with annotations that are related to technological aspects regarding a genomic feature or variant. For example, a property of a <a href="#classTechnologyPlatform">Technology Platform</a> class instance.</div>
1539
+ <div></div>
1540
+ </div>
1541
+ </p>
1542
+ <p>
1543
+ <h5 id="datatypePropertytechnologyPlatformDatatypeProperty">Datatype Property gfvo:technologyPlatformDatatypeProperty</h5>
1544
+ <div style="margin-left: 16px; margin-bottom: 16px">
1545
+ <div><i>Label:</i> technology platform datatype property</div>
1546
+ <div><i>Comment:</i> Property that is directly associated with <a href="#classTechnologyPlatform">Technology Platform</a> class instances.</div>
1547
+ <div></div>
1548
+ </div>
1549
+ </p>
1550
+ <p>
1551
+ <h5 id="datatypePropertytotalReads">Datatype Property gfvo:totalReads</h5>
1552
+ <div style="margin-left: 16px; margin-bottom: 16px">
1553
+ <div><i>Domain:</i> <a href="#classSequencedIndividual">SequencedIndividual</a></div>
1554
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#int">http://www.w3.org/2001/XMLSchema#int</a></div>
1555
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1556
+ <div><i>Label:</i> total reads</div>
1557
+ <div><i>Comment:</i> Total number of reads for a <a href="#classSequencedIndividual">Sequenced Individual</a>. When merging <a href="#classSet">Set</a>/<a href="#classFile">File</a> class instances, it should be noted whether the total number of reads needs to be updated based on the identity of sequenced individuals in the involved sets.</div>
1558
+ <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
1559
+ </div>
1560
+ </p>
1561
+ <p>
1562
+ <h5 id="datatypePropertyvariant_datatype_property">Datatype Property gfvo:variant_datatype_property</h5>
1563
+ <div style="margin-left: 16px; margin-bottom: 16px">
1564
+ <div><i>Label:</i> variant datatype property</div>
1565
+ <div><i>Comment:</i> A datatype property that is directly associated with <a href="#classVariant">Variant</a> class instances.</div>
1566
+ <div></div>
1567
+ </div>
1568
+ </p>
1569
+ <p>
1570
+ <h5 id="datatypePropertyvariationAnnotationDatatypeProperty">Datatype Property gfvo:variationAnnotationDatatypeProperty</h5>
1571
+ <div style="margin-left: 16px; margin-bottom: 16px">
1572
+ <div><i>Label:</i> variation annotation datatype property</div>
1573
+ <div><i>Comment:</i> A variation annotation datatype property is describing a datatype property of a <a href="#classVariant">Variant</a> or <a href="#classEffect">Effect</a> class instance.</div>
1574
+ <div></div>
1575
+ </div>
1576
+ </p>
1577
+ <p>
1578
+ <h5 id="datatypePropertyvcfVersion">Datatype Property gfvo:vcfVersion</h5>
1579
+ <div style="margin-left: 16px; margin-bottom: 16px">
1580
+ <div><i>Domain:</i> <a href="#classFile">File</a></div>
1581
+ <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#float">http://www.w3.org/2001/XMLSchema#float</a></div>
1582
+ <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
1583
+ <div><i>Label:</i> vcf version</div>
1584
+ <div><i>Comment:</i> Version of the VCF specification that defines the contents captured by the <a href="#classFile">File</a> class instance. The version number should be greater or equal than 4.0, but less than 5.0.</div>
1585
+ <div><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
1586
+ </div>
1587
+ </p>
1588
+ <!-- SNIP -->
1589
+
73
1590
  </div>
74
1591
  </div>
75
1592